Starting phenix.real_space_refine on Wed Sep 17 10:58:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xml_38481/09_2025/8xml_38481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xml_38481/09_2025/8xml_38481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xml_38481/09_2025/8xml_38481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xml_38481/09_2025/8xml_38481.map" model { file = "/net/cci-nas-00/data/ceres_data/8xml_38481/09_2025/8xml_38481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xml_38481/09_2025/8xml_38481.cif" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5279 2.51 5 N 1395 2.21 5 O 1508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8245 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1790 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1667 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2599 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1751 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 2.12, per 1000 atoms: 0.26 Number of scatterers: 8245 At special positions: 0 Unit cell: (88.81, 122.01, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1508 8.00 N 1395 7.00 C 5279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 428.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 35.6% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 44 through 62 removed outlier: 3.863A pdb=" N LEU R 51 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 92 Proline residue: R 89 - end of helix removed outlier: 3.623A pdb=" N THR R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 139 through 145 removed outlier: 4.054A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 Processing helix chain 'R' and resid 199 through 226 removed outlier: 6.123A pdb=" N ILE R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Proline residue: R 210 - end of helix removed outlier: 3.817A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 262 removed outlier: 4.260A pdb=" N LYS R 235 " --> pdb=" O HIS R 231 " (cutoff:3.500A) Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 286 through 301 removed outlier: 4.095A pdb=" N CYS R 293 " --> pdb=" O SER R 289 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 304 through 311 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.807A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.675A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.269A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.643A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.109A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.792A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.547A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.587A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.203A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.559A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.570A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.549A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.521A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.877A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.715A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.626A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.656A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.560A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.795A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.386A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.699A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR S 228 " --> pdb=" O PHE S 177 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 401 hydrogen bonds defined for protein. 1134 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.88 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: 2597 1.34 - 1.46: 1782 1.46 - 1.58: 3948 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 8416 Sorted by residual: bond pdb=" N ILE R 124 " pdb=" CA ILE R 124 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.77e+00 bond pdb=" N PHE R 117 " pdb=" CA PHE R 117 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.17e-02 7.31e+03 5.76e+00 bond pdb=" N THR R 125 " pdb=" CA THR R 125 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.28e-02 6.10e+03 4.91e+00 bond pdb=" N TYR R 118 " pdb=" CA TYR R 118 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.74e+00 bond pdb=" N PHE R 123 " pdb=" CA PHE R 123 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.60e+00 ... (remaining 8411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 11223 2.60 - 5.21: 159 5.21 - 7.81: 24 7.81 - 10.41: 4 10.41 - 13.01: 1 Bond angle restraints: 11411 Sorted by residual: angle pdb=" C LEU R 208 " pdb=" N ILE R 209 " pdb=" CA ILE R 209 " ideal model delta sigma weight residual 120.24 123.29 -3.05 6.30e-01 2.52e+00 2.34e+01 angle pdb=" N ASN R 296 " pdb=" CA ASN R 296 " pdb=" C ASN R 296 " ideal model delta sigma weight residual 113.25 117.98 -4.73 1.30e+00 5.92e-01 1.33e+01 angle pdb=" C TYR R 42 " pdb=" N CYS R 43 " pdb=" CA CYS R 43 " ideal model delta sigma weight residual 122.40 127.55 -5.15 1.45e+00 4.76e-01 1.26e+01 angle pdb=" C PHE R 250 " pdb=" N TRP R 251 " pdb=" CA TRP R 251 " ideal model delta sigma weight residual 122.23 116.81 5.42 1.57e+00 4.06e-01 1.19e+01 angle pdb=" CA ILE R 124 " pdb=" C ILE R 124 " pdb=" O ILE R 124 " ideal model delta sigma weight residual 120.95 117.52 3.43 1.04e+00 9.25e-01 1.09e+01 ... (remaining 11406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4783 17.87 - 35.74: 148 35.74 - 53.61: 17 53.61 - 71.48: 0 71.48 - 89.35: 3 Dihedral angle restraints: 4951 sinusoidal: 1843 harmonic: 3108 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 -177.65 -89.35 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CA TRP B 297 " pdb=" C TRP B 297 " pdb=" N ASP B 298 " pdb=" CA ASP B 298 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA THR R 103 " pdb=" C THR R 103 " pdb=" N VAL R 104 " pdb=" CA VAL R 104 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 4948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1013 0.055 - 0.110: 243 0.110 - 0.165: 59 0.165 - 0.220: 5 0.220 - 0.275: 4 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA THR R 125 " pdb=" N THR R 125 " pdb=" C THR R 125 " pdb=" CB THR R 125 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB ILE R 124 " pdb=" CA ILE R 124 " pdb=" CG1 ILE R 124 " pdb=" CG2 ILE R 124 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1321 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 111 " 0.015 2.00e-02 2.50e+03 1.43e-02 5.09e+00 pdb=" CG TRP S 111 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP S 111 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP S 111 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP S 111 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP S 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 111 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 111 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP S 111 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 209 " 0.037 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO R 210 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 210 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 210 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 289 " -0.022 2.00e-02 2.50e+03 1.51e-02 4.54e+00 pdb=" CG TYR B 289 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 289 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 289 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 289 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 289 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 289 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 289 " -0.011 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1532 2.77 - 3.30: 7355 3.30 - 3.83: 13764 3.83 - 4.37: 16232 4.37 - 4.90: 28707 Nonbonded interactions: 67590 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.291 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.302 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.313 3.040 nonbonded pdb=" ND2 ASN B 340 " pdb=" OD1 ASN G 59 " model vdw 2.381 3.120 ... (remaining 67585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.005 0.057 8417 Z= 0.254 Angle : 0.837 13.013 11413 Z= 0.481 Chirality : 0.053 0.275 1324 Planarity : 0.006 0.054 1424 Dihedral : 9.180 74.620 2940 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.22), residues: 1049 helix: -1.47 (0.22), residues: 345 sheet: -1.85 (0.28), residues: 283 loop : -2.24 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 68 TYR 0.032 0.003 TYR B 289 PHE 0.032 0.003 PHE R 290 TRP 0.038 0.003 TRP S 111 HIS 0.016 0.003 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 8416) covalent geometry : angle 0.83663 (11411) SS BOND : bond 0.00164 ( 1) SS BOND : angle 0.39143 ( 2) hydrogen bonds : bond 0.16480 ( 394) hydrogen bonds : angle 6.88776 ( 1134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 ASN cc_start: 0.8280 (m-40) cc_final: 0.7981 (m110) REVERT: R 68 SER cc_start: 0.8501 (t) cc_final: 0.7857 (t) REVERT: R 121 MET cc_start: 0.7407 (mmm) cc_final: 0.7141 (mmp) REVERT: R 235 LYS cc_start: 0.7488 (tttt) cc_final: 0.7001 (tttt) REVERT: A 263 SER cc_start: 0.9018 (m) cc_final: 0.8580 (t) REVERT: A 286 CYS cc_start: 0.8362 (t) cc_final: 0.8045 (t) REVERT: A 293 SER cc_start: 0.9023 (p) cc_final: 0.8411 (p) REVERT: A 304 GLN cc_start: 0.9122 (tt0) cc_final: 0.8878 (tt0) REVERT: A 306 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8833 (mm-40) REVERT: A 350 ASP cc_start: 0.8286 (t70) cc_final: 0.7953 (t0) REVERT: G 17 GLU cc_start: 0.8662 (tp30) cc_final: 0.8169 (tm-30) REVERT: S 83 MET cc_start: 0.8506 (mtm) cc_final: 0.8258 (mtm) REVERT: S 217 SER cc_start: 0.8312 (m) cc_final: 0.7709 (p) REVERT: S 219 LEU cc_start: 0.9357 (mp) cc_final: 0.9123 (mm) outliers start: 0 outliers final: 1 residues processed: 240 average time/residue: 0.6529 time to fit residues: 165.2307 Evaluate side-chains 157 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 HIS R 199 ASN R 230 ASN R 232 ASN A 188 HIS A 331 ASN B 13 GLN B 119 ASN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.078952 restraints weight = 14546.777| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.79 r_work: 0.2994 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8417 Z= 0.141 Angle : 0.608 12.492 11413 Z= 0.314 Chirality : 0.042 0.161 1324 Planarity : 0.004 0.034 1424 Dihedral : 4.989 36.461 1149 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 2.83 % Allowed : 13.15 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.25), residues: 1049 helix: 0.55 (0.27), residues: 347 sheet: -1.34 (0.29), residues: 271 loop : -1.82 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 214 TYR 0.022 0.002 TYR S 190 PHE 0.023 0.002 PHE R 48 TRP 0.017 0.002 TRP S 111 HIS 0.008 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8416) covalent geometry : angle 0.60817 (11411) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.20350 ( 2) hydrogen bonds : bond 0.04046 ( 394) hydrogen bonds : angle 4.77282 ( 1134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 SER cc_start: 0.9153 (m) cc_final: 0.8659 (t) REVERT: A 275 GLU cc_start: 0.9308 (tp30) cc_final: 0.8948 (tp30) REVERT: A 276 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8608 (pm20) REVERT: A 298 GLU cc_start: 0.8837 (tt0) cc_final: 0.8507 (pt0) REVERT: A 304 GLN cc_start: 0.9109 (tt0) cc_final: 0.8829 (tt0) REVERT: A 315 ASP cc_start: 0.8699 (p0) cc_final: 0.8453 (p0) REVERT: A 341 ASP cc_start: 0.8443 (m-30) cc_final: 0.7919 (t70) REVERT: B 19 ARG cc_start: 0.8274 (ttp-110) cc_final: 0.7957 (ttp80) REVERT: B 215 GLU cc_start: 0.8118 (pt0) cc_final: 0.7897 (pt0) REVERT: S 217 SER cc_start: 0.8339 (m) cc_final: 0.7760 (p) REVERT: S 219 LEU cc_start: 0.9332 (mp) cc_final: 0.9006 (mm) outliers start: 25 outliers final: 8 residues processed: 180 average time/residue: 0.6725 time to fit residues: 127.7907 Evaluate side-chains 148 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 53 ASN R 76 ASN R 199 ASN ** R 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079142 restraints weight = 14479.076| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.77 r_work: 0.2990 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8417 Z= 0.120 Angle : 0.570 11.352 11413 Z= 0.290 Chirality : 0.041 0.143 1324 Planarity : 0.003 0.031 1424 Dihedral : 4.538 20.435 1147 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 14.51 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.26), residues: 1049 helix: 1.28 (0.29), residues: 347 sheet: -1.16 (0.30), residues: 260 loop : -1.58 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 227 TYR 0.021 0.001 TYR S 190 PHE 0.020 0.001 PHE R 250 TRP 0.015 0.001 TRP S 111 HIS 0.006 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8416) covalent geometry : angle 0.56983 (11411) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.21552 ( 2) hydrogen bonds : bond 0.03643 ( 394) hydrogen bonds : angle 4.46058 ( 1134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 50 LEU cc_start: 0.8807 (tm) cc_final: 0.8604 (tp) REVERT: R 238 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7631 (ttm-80) REVERT: A 263 SER cc_start: 0.9136 (m) cc_final: 0.8640 (t) REVERT: A 269 ASN cc_start: 0.7972 (t0) cc_final: 0.7744 (m110) REVERT: A 275 GLU cc_start: 0.9304 (tp30) cc_final: 0.8946 (tp30) REVERT: A 276 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8689 (mp0) REVERT: A 298 GLU cc_start: 0.8859 (tt0) cc_final: 0.8530 (pt0) REVERT: A 315 ASP cc_start: 0.8737 (p0) cc_final: 0.8468 (p0) REVERT: A 341 ASP cc_start: 0.8439 (m-30) cc_final: 0.8000 (t70) REVERT: B 197 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7671 (mtp85) REVERT: B 215 GLU cc_start: 0.8169 (pt0) cc_final: 0.7926 (pt0) REVERT: G 46 LYS cc_start: 0.9034 (pmtt) cc_final: 0.8824 (mmmm) REVERT: S 82 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8109 (tp-100) REVERT: S 155 VAL cc_start: 0.8021 (t) cc_final: 0.7815 (m) REVERT: S 219 LEU cc_start: 0.9262 (mp) cc_final: 0.8848 (mm) outliers start: 28 outliers final: 9 residues processed: 173 average time/residue: 0.6349 time to fit residues: 116.2165 Evaluate side-chains 147 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 100 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 304 GLN B 32 GLN B 259 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.110750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.079698 restraints weight = 14865.275| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.75 r_work: 0.2972 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8417 Z= 0.130 Angle : 0.565 12.774 11413 Z= 0.286 Chirality : 0.041 0.144 1324 Planarity : 0.003 0.039 1424 Dihedral : 4.411 19.482 1147 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 3.17 % Allowed : 15.76 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.26), residues: 1049 helix: 1.56 (0.29), residues: 349 sheet: -1.02 (0.30), residues: 260 loop : -1.31 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 24 TYR 0.027 0.001 TYR A 287 PHE 0.016 0.001 PHE R 214 TRP 0.009 0.001 TRP S 111 HIS 0.004 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8416) covalent geometry : angle 0.56545 (11411) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.19522 ( 2) hydrogen bonds : bond 0.03497 ( 394) hydrogen bonds : angle 4.33826 ( 1134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 238 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7657 (ttm-80) REVERT: R 305 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8232 (mm-30) REVERT: A 263 SER cc_start: 0.9147 (m) cc_final: 0.8630 (t) REVERT: A 269 ASN cc_start: 0.8053 (t0) cc_final: 0.7810 (m110) REVERT: A 275 GLU cc_start: 0.9278 (tp30) cc_final: 0.9009 (tp30) REVERT: A 276 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: A 290 TYR cc_start: 0.8046 (t80) cc_final: 0.7478 (t80) REVERT: A 298 GLU cc_start: 0.8911 (tt0) cc_final: 0.8668 (tt0) REVERT: A 315 ASP cc_start: 0.8794 (p0) cc_final: 0.8499 (p0) REVERT: A 341 ASP cc_start: 0.8455 (m-30) cc_final: 0.7997 (t0) REVERT: B 19 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.8110 (ttp80) REVERT: B 215 GLU cc_start: 0.8187 (pt0) cc_final: 0.7932 (pt0) REVERT: B 259 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: B 290 ASP cc_start: 0.8154 (m-30) cc_final: 0.7952 (m-30) REVERT: G 46 LYS cc_start: 0.9017 (pmtt) cc_final: 0.8808 (mmmm) REVERT: S 155 VAL cc_start: 0.8145 (t) cc_final: 0.7939 (m) REVERT: S 219 LEU cc_start: 0.9264 (mp) cc_final: 0.8789 (mm) outliers start: 28 outliers final: 15 residues processed: 166 average time/residue: 0.6084 time to fit residues: 107.0208 Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 199 ASN Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 55 optimal weight: 0.0770 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 259 GLN B 295 ASN S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077540 restraints weight = 14645.547| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.77 r_work: 0.2988 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8417 Z= 0.128 Angle : 0.564 12.188 11413 Z= 0.284 Chirality : 0.041 0.137 1324 Planarity : 0.003 0.044 1424 Dihedral : 4.340 18.366 1147 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Rotamer: Outliers : 3.51 % Allowed : 17.01 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.26), residues: 1049 helix: 1.69 (0.29), residues: 349 sheet: -0.95 (0.30), residues: 260 loop : -1.18 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 24 TYR 0.026 0.002 TYR A 287 PHE 0.015 0.001 PHE R 214 TRP 0.020 0.001 TRP R 99 HIS 0.007 0.001 HIS R 310 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8416) covalent geometry : angle 0.56386 (11411) SS BOND : bond 0.00100 ( 1) SS BOND : angle 0.90542 ( 2) hydrogen bonds : bond 0.03365 ( 394) hydrogen bonds : angle 4.28564 ( 1134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 121 MET cc_start: 0.7206 (tpp) cc_final: 0.6798 (mmp) REVERT: R 238 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7677 (ttm-80) REVERT: R 251 TRP cc_start: 0.7785 (m100) cc_final: 0.7288 (m-90) REVERT: R 292 HIS cc_start: 0.7228 (t70) cc_final: 0.6687 (t70) REVERT: R 305 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8248 (mm-30) REVERT: A 269 ASN cc_start: 0.8078 (t0) cc_final: 0.7850 (m110) REVERT: A 275 GLU cc_start: 0.9291 (tp30) cc_final: 0.9022 (tp30) REVERT: A 276 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8647 (pm20) REVERT: A 287 TYR cc_start: 0.7818 (m-10) cc_final: 0.7390 (m-10) REVERT: A 290 TYR cc_start: 0.8057 (t80) cc_final: 0.7516 (t80) REVERT: A 298 GLU cc_start: 0.8925 (tt0) cc_final: 0.8692 (tt0) REVERT: A 306 GLN cc_start: 0.8787 (tt0) cc_final: 0.8431 (mt0) REVERT: A 315 ASP cc_start: 0.8796 (p0) cc_final: 0.8499 (p0) REVERT: A 328 ASP cc_start: 0.8136 (m-30) cc_final: 0.7847 (m-30) REVERT: A 341 ASP cc_start: 0.8410 (m-30) cc_final: 0.7917 (t0) REVERT: B 19 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.8034 (ttp80) REVERT: B 197 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7645 (mtp85) REVERT: B 215 GLU cc_start: 0.8154 (pt0) cc_final: 0.7896 (pt0) REVERT: B 290 ASP cc_start: 0.8161 (m-30) cc_final: 0.7955 (m-30) REVERT: G 46 LYS cc_start: 0.9011 (pmtt) cc_final: 0.8792 (mmmm) REVERT: S 82 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8006 (tp-100) REVERT: S 219 LEU cc_start: 0.9271 (mp) cc_final: 0.8785 (mm) outliers start: 31 outliers final: 16 residues processed: 162 average time/residue: 0.6160 time to fit residues: 105.7538 Evaluate side-chains 147 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 199 ASN Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 331 ASN B 259 GLN S 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075268 restraints weight = 14586.518| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.75 r_work: 0.2935 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8417 Z= 0.169 Angle : 0.583 13.085 11413 Z= 0.295 Chirality : 0.042 0.137 1324 Planarity : 0.004 0.048 1424 Dihedral : 4.484 17.688 1147 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 3.63 % Allowed : 17.12 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1049 helix: 1.75 (0.29), residues: 349 sheet: -0.93 (0.30), residues: 266 loop : -1.08 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 24 TYR 0.023 0.002 TYR S 190 PHE 0.017 0.001 PHE R 214 TRP 0.012 0.001 TRP R 251 HIS 0.004 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8416) covalent geometry : angle 0.58292 (11411) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.52711 ( 2) hydrogen bonds : bond 0.03578 ( 394) hydrogen bonds : angle 4.34740 ( 1134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 81 ASP cc_start: 0.7632 (t70) cc_final: 0.7316 (t70) REVERT: R 121 MET cc_start: 0.7202 (tpp) cc_final: 0.6866 (mmp) REVERT: R 251 TRP cc_start: 0.7760 (m100) cc_final: 0.7201 (m-90) REVERT: R 292 HIS cc_start: 0.7111 (t70) cc_final: 0.6082 (t70) REVERT: R 305 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8226 (mm-30) REVERT: A 269 ASN cc_start: 0.8168 (t0) cc_final: 0.7808 (m110) REVERT: A 275 GLU cc_start: 0.9287 (tp30) cc_final: 0.8995 (tp30) REVERT: A 276 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: A 298 GLU cc_start: 0.8958 (tt0) cc_final: 0.8719 (tt0) REVERT: A 306 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: A 315 ASP cc_start: 0.8820 (p0) cc_final: 0.8533 (p0) REVERT: A 341 ASP cc_start: 0.8426 (m-30) cc_final: 0.8062 (t0) REVERT: G 46 LYS cc_start: 0.9031 (pmtt) cc_final: 0.8801 (mmmm) REVERT: S 219 LEU cc_start: 0.9293 (mp) cc_final: 0.8901 (mm) outliers start: 32 outliers final: 23 residues processed: 166 average time/residue: 0.6334 time to fit residues: 111.3203 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 88 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: ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 259 GLN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.076234 restraints weight = 14805.565| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.79 r_work: 0.2939 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8417 Z= 0.132 Angle : 0.575 13.158 11413 Z= 0.290 Chirality : 0.041 0.136 1324 Planarity : 0.004 0.049 1424 Dihedral : 4.399 17.013 1147 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 2.95 % Allowed : 18.59 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1049 helix: 1.83 (0.29), residues: 348 sheet: -0.89 (0.29), residues: 267 loop : -1.02 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 24 TYR 0.030 0.002 TYR S 190 PHE 0.023 0.001 PHE R 46 TRP 0.014 0.001 TRP R 99 HIS 0.003 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8416) covalent geometry : angle 0.57540 (11411) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.57201 ( 2) hydrogen bonds : bond 0.03385 ( 394) hydrogen bonds : angle 4.28226 ( 1134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 81 ASP cc_start: 0.7630 (t70) cc_final: 0.7162 (t70) REVERT: R 121 MET cc_start: 0.7231 (tpp) cc_final: 0.6844 (mmp) REVERT: R 127 MET cc_start: 0.8032 (mtp) cc_final: 0.7701 (mtm) REVERT: R 238 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7651 (ttm-80) REVERT: R 251 TRP cc_start: 0.7674 (m100) cc_final: 0.7088 (m-90) REVERT: R 292 HIS cc_start: 0.7166 (t70) cc_final: 0.6298 (t70) REVERT: R 293 CYS cc_start: 0.7244 (m) cc_final: 0.6795 (p) REVERT: R 305 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 269 ASN cc_start: 0.8140 (t0) cc_final: 0.7819 (m110) REVERT: A 275 GLU cc_start: 0.9294 (tp30) cc_final: 0.9060 (tp30) REVERT: A 276 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: A 287 TYR cc_start: 0.7781 (m-10) cc_final: 0.7429 (m-10) REVERT: A 298 GLU cc_start: 0.8950 (tt0) cc_final: 0.8612 (pt0) REVERT: A 315 ASP cc_start: 0.8844 (p0) cc_final: 0.8528 (p0) REVERT: A 341 ASP cc_start: 0.8436 (m-30) cc_final: 0.8094 (t0) REVERT: B 19 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.8062 (ttp80) REVERT: B 214 ARG cc_start: 0.8669 (mmp80) cc_final: 0.8369 (mmt180) REVERT: B 215 GLU cc_start: 0.8148 (pt0) cc_final: 0.7233 (pp20) REVERT: B 219 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8332 (mmt-90) REVERT: G 46 LYS cc_start: 0.9039 (pmtt) cc_final: 0.8799 (mmmm) REVERT: S 219 LEU cc_start: 0.9300 (mp) cc_final: 0.8878 (mm) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 0.6207 time to fit residues: 105.0483 Evaluate side-chains 156 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077092 restraints weight = 14694.008| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 2.78 r_work: 0.2954 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8417 Z= 0.123 Angle : 0.573 10.371 11413 Z= 0.292 Chirality : 0.041 0.136 1324 Planarity : 0.004 0.050 1424 Dihedral : 4.312 16.679 1147 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 3.06 % Allowed : 19.16 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.26), residues: 1049 helix: 1.77 (0.29), residues: 349 sheet: -0.75 (0.30), residues: 260 loop : -1.01 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 24 TYR 0.028 0.002 TYR S 190 PHE 0.024 0.001 PHE R 46 TRP 0.018 0.001 TRP R 99 HIS 0.003 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8416) covalent geometry : angle 0.57326 (11411) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.54237 ( 2) hydrogen bonds : bond 0.03347 ( 394) hydrogen bonds : angle 4.24130 ( 1134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 TRP cc_start: 0.4762 (p-90) cc_final: 0.4026 (t60) REVERT: R 121 MET cc_start: 0.7256 (tpp) cc_final: 0.6829 (mmp) REVERT: R 251 TRP cc_start: 0.7669 (m100) cc_final: 0.7171 (m-90) REVERT: R 292 HIS cc_start: 0.7105 (t70) cc_final: 0.6363 (t70) REVERT: R 293 CYS cc_start: 0.7354 (m) cc_final: 0.7111 (t) REVERT: R 305 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 269 ASN cc_start: 0.8108 (t0) cc_final: 0.7901 (m110) REVERT: A 275 GLU cc_start: 0.9267 (tp30) cc_final: 0.9032 (tp30) REVERT: A 276 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8715 (pm20) REVERT: A 298 GLU cc_start: 0.8912 (tt0) cc_final: 0.8586 (pt0) REVERT: A 315 ASP cc_start: 0.8834 (p0) cc_final: 0.8482 (p0) REVERT: A 341 ASP cc_start: 0.8415 (m-30) cc_final: 0.8083 (t0) REVERT: B 19 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.8053 (ttp80) REVERT: B 215 GLU cc_start: 0.8118 (pt0) cc_final: 0.7169 (pp20) REVERT: B 219 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8319 (mmt-90) REVERT: G 46 LYS cc_start: 0.9011 (pmtt) cc_final: 0.8770 (mmmm) REVERT: S 219 LEU cc_start: 0.9287 (mp) cc_final: 0.8877 (mm) outliers start: 27 outliers final: 18 residues processed: 159 average time/residue: 0.6376 time to fit residues: 107.1819 Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 199 ASN Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 259 GLN S 113 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079116 restraints weight = 14507.297| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.76 r_work: 0.2960 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8417 Z= 0.115 Angle : 0.571 13.624 11413 Z= 0.287 Chirality : 0.041 0.137 1324 Planarity : 0.004 0.054 1424 Dihedral : 4.206 16.230 1147 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 2.61 % Allowed : 20.07 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.26), residues: 1049 helix: 1.83 (0.29), residues: 349 sheet: -0.73 (0.29), residues: 264 loop : -0.94 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 24 TYR 0.028 0.001 TYR S 190 PHE 0.024 0.001 PHE R 46 TRP 0.014 0.001 TRP R 99 HIS 0.002 0.001 HIS R 292 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8416) covalent geometry : angle 0.57079 (11411) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.39689 ( 2) hydrogen bonds : bond 0.03241 ( 394) hydrogen bonds : angle 4.16904 ( 1134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 TRP cc_start: 0.4936 (p-90) cc_final: 0.4225 (t60) REVERT: R 121 MET cc_start: 0.7199 (tpp) cc_final: 0.6758 (mmp) REVERT: R 127 MET cc_start: 0.7947 (mtp) cc_final: 0.7561 (mtm) REVERT: R 250 PHE cc_start: 0.7722 (m-10) cc_final: 0.7455 (m-10) REVERT: R 251 TRP cc_start: 0.7677 (m100) cc_final: 0.7212 (m-90) REVERT: R 292 HIS cc_start: 0.7119 (t70) cc_final: 0.6472 (t70) REVERT: R 293 CYS cc_start: 0.7253 (m) cc_final: 0.6949 (p) REVERT: R 305 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8146 (mm-30) REVERT: A 275 GLU cc_start: 0.9250 (tp30) cc_final: 0.9032 (tp30) REVERT: A 276 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8685 (pm20) REVERT: A 287 TYR cc_start: 0.7623 (m-10) cc_final: 0.7183 (m-80) REVERT: A 298 GLU cc_start: 0.8893 (tt0) cc_final: 0.8590 (pt0) REVERT: A 306 GLN cc_start: 0.8651 (tt0) cc_final: 0.8054 (mt0) REVERT: A 341 ASP cc_start: 0.8385 (m-30) cc_final: 0.7891 (t0) REVERT: B 215 GLU cc_start: 0.8111 (pt0) cc_final: 0.7264 (pp20) REVERT: B 219 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8223 (mtt-85) REVERT: G 46 LYS cc_start: 0.9001 (pmtt) cc_final: 0.8763 (mmmm) REVERT: S 120 SER cc_start: 0.8716 (t) cc_final: 0.8380 (m) REVERT: S 219 LEU cc_start: 0.9297 (mp) cc_final: 0.8887 (mm) outliers start: 23 outliers final: 17 residues processed: 161 average time/residue: 0.6399 time to fit residues: 109.2473 Evaluate side-chains 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 199 ASN Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 76 optimal weight: 0.0030 chunk 100 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN S 113 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.108678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076677 restraints weight = 14469.575| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.75 r_work: 0.2932 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8417 Z= 0.165 Angle : 0.607 12.978 11413 Z= 0.308 Chirality : 0.042 0.137 1324 Planarity : 0.004 0.060 1424 Dihedral : 4.367 17.587 1147 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.93 % Allowed : 21.43 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.26), residues: 1049 helix: 1.84 (0.29), residues: 348 sheet: -0.73 (0.29), residues: 281 loop : -0.92 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 24 TYR 0.028 0.002 TYR S 190 PHE 0.023 0.001 PHE R 46 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8416) covalent geometry : angle 0.60716 (11411) SS BOND : bond 0.00000 ( 1) SS BOND : angle 0.18823 ( 2) hydrogen bonds : bond 0.03531 ( 394) hydrogen bonds : angle 4.23463 ( 1134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 TRP cc_start: 0.5175 (p-90) cc_final: 0.4529 (t60) REVERT: R 121 MET cc_start: 0.7255 (tpp) cc_final: 0.6825 (mmp) REVERT: R 127 MET cc_start: 0.7907 (mtp) cc_final: 0.7559 (mtm) REVERT: R 251 TRP cc_start: 0.7659 (m100) cc_final: 0.7124 (m-90) REVERT: R 292 HIS cc_start: 0.7211 (t70) cc_final: 0.6486 (t70) REVERT: R 293 CYS cc_start: 0.7251 (m) cc_final: 0.6927 (p) REVERT: R 305 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 275 GLU cc_start: 0.9266 (tp30) cc_final: 0.9030 (tp30) REVERT: A 276 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8713 (pm20) REVERT: A 298 GLU cc_start: 0.8900 (tt0) cc_final: 0.8576 (pt0) REVERT: A 306 GLN cc_start: 0.8701 (tt0) cc_final: 0.8116 (mt0) REVERT: A 341 ASP cc_start: 0.8399 (m-30) cc_final: 0.8039 (t0) REVERT: B 19 ARG cc_start: 0.8316 (ttp80) cc_final: 0.8115 (ttp80) REVERT: B 197 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7714 (mmp80) REVERT: B 215 GLU cc_start: 0.8034 (pt0) cc_final: 0.7613 (pp20) REVERT: B 219 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8181 (mtt-85) REVERT: G 20 LYS cc_start: 0.9297 (ttmm) cc_final: 0.9094 (tmmt) REVERT: S 120 SER cc_start: 0.8747 (t) cc_final: 0.8389 (m) REVERT: S 219 LEU cc_start: 0.9282 (mp) cc_final: 0.8871 (mm) outliers start: 17 outliers final: 12 residues processed: 156 average time/residue: 0.6643 time to fit residues: 109.6656 Evaluate side-chains 152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 198 THR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 100 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.109906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.078375 restraints weight = 14659.295| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.76 r_work: 0.2960 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8417 Z= 0.126 Angle : 0.615 15.498 11413 Z= 0.304 Chirality : 0.042 0.262 1324 Planarity : 0.004 0.057 1424 Dihedral : 4.274 19.359 1147 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.04 % Allowed : 21.66 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.26), residues: 1049 helix: 1.82 (0.29), residues: 348 sheet: -0.58 (0.30), residues: 261 loop : -0.92 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 24 TYR 0.029 0.001 TYR S 190 PHE 0.024 0.001 PHE R 46 TRP 0.011 0.001 TRP R 99 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8416) covalent geometry : angle 0.61458 (11411) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.24271 ( 2) hydrogen bonds : bond 0.03346 ( 394) hydrogen bonds : angle 4.19768 ( 1134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3561.16 seconds wall clock time: 61 minutes 28.58 seconds (3688.58 seconds total)