Starting phenix.real_space_refine on Thu Jul 2 16:47:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.map" model { file = "/net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w40_32298/07_2026/7w40_32298.cif" } resolution = 3.0 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= 0.000 sd= 0.003 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 57 5.16 5 C 5882 2.51 5 N 1573 2.21 5 O 1724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9236 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2280 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 14, 'TRANS': 286} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2330 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2409 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 5, 'TRANS': 309} Chain: "D" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 365 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "H" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 81 Unusual residues: {'BAL': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'DPN:plan-2': 1, 'BAL:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9236 At special positions: 0 Unit cell: (111.54, 112.554, 128.778, 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 57 16.00 O 1724 8.00 N 1573 7.00 C 5882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 220.6 milliseconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DPN E 1 " Input volumes are d-peptide like pdb=" CB BAL E 6 " Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 39.2% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 37 through 69 Proline residue: A 44 - end of helix removed outlier: 4.306A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 103 removed outlier: 3.600A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 108 through 144 removed outlier: 4.061A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Proline residue: A 117 - end of helix removed outlier: 3.523A pdb=" N THR A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 173 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 205 through 219 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.549A pdb=" N TYR A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 252 through 290 removed outlier: 3.717A pdb=" N LYS A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Proline residue: A 279 - end of helix removed outlier: 3.743A pdb=" N LEU A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 326 removed outlier: 3.593A pdb=" N ASN A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Proline residue: A 319 - end of helix removed outlier: 3.847A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.822A pdb=" N ARG B 38 " --> pdb=" O GLU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 54 through 64 Processing helix chain 'B' and resid 68 through 88 removed outlier: 4.687A pdb=" N LYS B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.750A pdb=" N GLU B 150 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 175 through 181 Processing helix chain 'B' and resid 212 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 275 through 286 removed outlier: 4.434A pdb=" N MET B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 4.171A pdb=" N TYR B 291 " --> pdb=" O HIS B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.509A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197 removed outlier: 8.867A pdb=" N VAL A 294 " --> pdb=" O PRO A 183 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N HIS A 185 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196 removed outlier: 6.347A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 225 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 226 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE B 272 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 228 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ASN B 274 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 230 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.739A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.697A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.072A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.660A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.895A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.286A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.595A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.730A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.327A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 148 removed outlier: 3.616A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1272 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: 1.08 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2015 1.33 - 1.45: 2197 1.45 - 1.57: 5142 1.57 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 9440 Sorted by residual: bond pdb=" CG TRP E 3 " pdb=" CD2 TRP E 3 " ideal model delta sigma weight residual 1.433 1.333 0.100 1.80e-02 3.09e+03 3.07e+01 bond pdb=" CB DPN E 1 " pdb=" CG DPN E 1 " ideal model delta sigma weight residual 1.501 1.391 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" CB PHE E 8 " pdb=" CG PHE E 8 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.57e+01 bond pdb=" CG HIS E 7 " pdb=" ND1 HIS E 7 " ideal model delta sigma weight residual 1.378 1.324 0.054 1.10e-02 8.26e+03 2.37e+01 bond pdb=" C VAL A 266 " pdb=" O VAL A 266 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.17e-02 7.31e+03 2.19e+01 ... (remaining 9435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10547 1.64 - 3.28: 1904 3.28 - 4.92: 296 4.92 - 6.56: 40 6.56 - 8.20: 12 Bond angle restraints: 12799 Sorted by residual: angle pdb=" N ASP C 247 " pdb=" CA ASP C 247 " pdb=" C ASP C 247 " ideal model delta sigma weight residual 110.35 102.15 8.20 1.36e+00 5.41e-01 3.64e+01 angle pdb=" N ALA A 176 " pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 113.97 106.80 7.17 1.28e+00 6.10e-01 3.14e+01 angle pdb=" CA GLY H 114 " pdb=" C GLY H 114 " pdb=" O GLY H 114 " ideal model delta sigma weight residual 121.88 117.85 4.03 7.80e-01 1.64e+00 2.67e+01 angle pdb=" N LEU A 205 " pdb=" CA LEU A 205 " pdb=" C LEU A 205 " ideal model delta sigma weight residual 113.55 107.06 6.49 1.26e+00 6.30e-01 2.66e+01 angle pdb=" N ARG C 48 " pdb=" CA ARG C 48 " pdb=" C ARG C 48 " ideal model delta sigma weight residual 113.23 106.84 6.39 1.24e+00 6.50e-01 2.65e+01 ... (remaining 12794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 5102 16.73 - 33.46: 403 33.46 - 50.20: 78 50.20 - 66.93: 16 66.93 - 83.66: 2 Dihedral angle restraints: 5601 sinusoidal: 2153 harmonic: 3448 Sorted by residual: dihedral pdb=" C TYR H 235 " pdb=" N TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual -122.60 -140.20 17.60 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 36.36 56.64 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CA TYR H 235 " pdb=" CB TYR H 235 " ideal model delta harmonic sigma weight residual 122.80 139.06 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 5598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1285 0.135 - 0.270: 145 0.270 - 0.405: 8 0.405 - 0.540: 0 0.540 - 0.675: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA TYR H 235 " pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CB TYR H 235 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CA LEU C 79 " pdb=" N LEU C 79 " pdb=" C LEU C 79 " pdb=" CB LEU C 79 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LEU H 4 " pdb=" N LEU H 4 " pdb=" C LEU H 4 " pdb=" CB LEU H 4 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1436 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 175 " 0.016 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR H 175 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR H 175 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR H 175 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR H 175 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR H 175 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR H 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 175 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 127 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C LYS C 127 " -0.055 2.00e-02 2.50e+03 pdb=" O LYS C 127 " 0.021 2.00e-02 2.50e+03 pdb=" N THR C 128 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 315 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C VAL C 315 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL C 315 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 316 " -0.017 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1996 2.79 - 3.32: 8658 3.32 - 3.85: 14852 3.85 - 4.37: 18476 4.37 - 4.90: 31094 Nonbonded interactions: 75076 Sorted by model distance: nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASP C 205 " pdb=" OG SER C 207 " model vdw 2.290 3.040 nonbonded pdb=" NE ARG C 283 " pdb=" OD1 ASP C 298 " model vdw 2.309 3.120 nonbonded pdb=" O SER C 67 " pdb=" OG SER C 67 " model vdw 2.322 3.040 nonbonded pdb=" OG SER C 281 " pdb=" OD2 ASP D 48 " model vdw 2.341 3.040 ... (remaining 75071 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: 1.310 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.710 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:7.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 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 : 0.011 0.117 9443 Z= 0.717 Angle : 1.290 8.202 12805 Z= 0.928 Chirality : 0.085 0.675 1439 Planarity : 0.006 0.053 1630 Dihedral : 12.497 83.658 3370 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 3.84 % Favored : 94.24 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.42 (0.23), residues: 1162 helix: 0.42 (0.25), residues: 411 sheet: 0.10 (0.31), residues: 286 loop : -1.08 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 259 TYR 0.056 0.003 TYR H 175 PHE 0.030 0.003 PHE C 199 TRP 0.036 0.003 TRP C 82 HIS 0.009 0.002 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.01062 / 0.72 ( 9440) covalent geometry : angle 1.28847 / 0.93 (12799) SS BOND : bond 0.02111 / 1.47 ( 3) SS BOND : angle 3.05823 / 2.50 ( 6) hydrogen bonds : bond 0.17159 / 12.05 ( 449) hydrogen bonds : angle 6.82059 / 5.24 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 SER cc_start: 0.5579 (t) cc_final: 0.5324 (m) REVERT: B 26 ASP cc_start: 0.7878 (m-30) cc_final: 0.7267 (m-30) REVERT: B 60 ARG cc_start: 0.6721 (ttp80) cc_final: 0.6094 (mmm160) REVERT: B 83 ILE cc_start: 0.6982 (mp) cc_final: 0.6747 (mp) REVERT: B 259 ILE cc_start: 0.7714 (pt) cc_final: 0.7485 (pt) REVERT: B 322 LYS cc_start: 0.7322 (mtpp) cc_final: 0.6756 (tptt) REVERT: B 332 THR cc_start: 0.7611 (t) cc_final: 0.7182 (m) REVERT: B 348 ILE cc_start: 0.6745 (mm) cc_final: 0.6508 (mt) outliers start: 19 outliers final: 3 residues processed: 246 average time/residue: 0.5160 time to fit residues: 135.5494 Evaluate side-chains 145 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 296 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 HIS C 75 GLN H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.212215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.169387 restraints weight = 9665.648| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.07 r_work: 0.3993 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9443 Z= 0.148 Angle : 0.648 9.382 12805 Z= 0.339 Chirality : 0.043 0.298 1439 Planarity : 0.004 0.049 1630 Dihedral : 5.470 46.360 1302 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.45 % Allowed : 13.45 % Favored : 82.10 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.56 (0.24), residues: 1162 helix: 1.76 (0.24), residues: 417 sheet: 0.39 (0.31), residues: 279 loop : -0.90 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.052 0.002 TYR H 235 PHE 0.016 0.002 PHE B 201 TRP 0.020 0.002 TRP C 82 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 ( 9440) covalent geometry : angle 0.64672 / 0.34 (12799) SS BOND : bond 0.00427 / 0.26 ( 3) SS BOND : angle 1.84771 / 1.34 ( 6) hydrogen bonds : bond 0.05193 / 3.79 ( 449) hydrogen bonds : angle 4.75707 / 3.63 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7753 (mptt) cc_final: 0.7176 (mttp) REVERT: B 60 ARG cc_start: 0.7020 (ttp80) cc_final: 0.5511 (mmp-170) REVERT: B 202 ARG cc_start: 0.7065 (mtp85) cc_final: 0.6435 (ptm160) REVERT: B 303 GLN cc_start: 0.6647 (tp40) cc_final: 0.6207 (tp40) REVERT: B 322 LYS cc_start: 0.7605 (mtpp) cc_final: 0.6818 (tptt) REVERT: C 76 ASP cc_start: 0.7137 (p0) cc_final: 0.5910 (t0) REVERT: C 129 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6755 (ttt90) REVERT: C 188 MET cc_start: 0.7109 (mmm) cc_final: 0.6864 (mmp) REVERT: C 197 ARG cc_start: 0.6886 (mtp85) cc_final: 0.6431 (mmp80) REVERT: H 172 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7644 (t) REVERT: H 244 LYS cc_start: 0.8059 (tttt) cc_final: 0.7701 (ttpp) outliers start: 44 outliers final: 20 residues processed: 178 average time/residue: 0.5861 time to fit residues: 110.5928 Evaluate side-chains 144 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 172 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN B 336 ASN C 142 HIS H 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.168327 restraints weight = 9609.670| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.10 r_work: 0.3932 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9443 Z= 0.158 Angle : 0.630 8.537 12805 Z= 0.331 Chirality : 0.044 0.254 1439 Planarity : 0.005 0.043 1630 Dihedral : 5.705 71.353 1302 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.46 % Allowed : 15.77 % Favored : 78.77 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.69 (0.24), residues: 1162 helix: 1.96 (0.25), residues: 419 sheet: 0.30 (0.30), residues: 284 loop : -0.85 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 314 TYR 0.025 0.002 TYR B 285 PHE 0.018 0.002 PHE C 253 TRP 0.015 0.002 TRP C 82 HIS 0.005 0.002 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9440) covalent geometry : angle 0.62832 / 0.33 (12799) SS BOND : bond 0.00531 / 0.35 ( 3) SS BOND : angle 2.23919 / 1.44 ( 6) hydrogen bonds : bond 0.05048 / 3.67 ( 449) hydrogen bonds : angle 4.57872 / 3.48 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6883 (tt) REVERT: A 286 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6372 (t80) REVERT: B 38 ARG cc_start: 0.7354 (mtp-110) cc_final: 0.7086 (mtp85) REVERT: B 60 ARG cc_start: 0.6995 (ttp80) cc_final: 0.5515 (mmp-170) REVERT: B 202 ARG cc_start: 0.7194 (mtp85) cc_final: 0.6503 (ptm160) REVERT: B 280 GLU cc_start: 0.7905 (tp30) cc_final: 0.7409 (tm-30) REVERT: B 322 LYS cc_start: 0.7701 (mtpp) cc_final: 0.6889 (tptt) REVERT: B 335 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: C 52 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7555 (mtp85) REVERT: C 76 ASP cc_start: 0.7412 (p0) cc_final: 0.7043 (p0) REVERT: C 129 ARG cc_start: 0.7259 (mtt180) cc_final: 0.7004 (ttt90) REVERT: C 188 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6938 (mmp) REVERT: C 197 ARG cc_start: 0.6976 (mtp85) cc_final: 0.6539 (mmp80) REVERT: C 269 ILE cc_start: 0.7112 (OUTLIER) cc_final: 0.6660 (mm) REVERT: H 46 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: H 235 TYR cc_start: 0.4530 (OUTLIER) cc_final: 0.4074 (t80) REVERT: H 244 LYS cc_start: 0.8059 (tttt) cc_final: 0.7806 (tttm) outliers start: 54 outliers final: 26 residues processed: 171 average time/residue: 0.5930 time to fit residues: 107.3391 Evaluate side-chains 149 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 286 TYR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 0.0000 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN ** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.204413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.167424 restraints weight = 9758.212| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.73 r_work: 0.3915 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9443 Z= 0.166 Angle : 0.640 8.068 12805 Z= 0.331 Chirality : 0.044 0.261 1439 Planarity : 0.004 0.042 1630 Dihedral : 5.458 64.315 1299 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.36 % Allowed : 17.39 % Favored : 77.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.77 (0.24), residues: 1162 helix: 2.07 (0.25), residues: 413 sheet: 0.35 (0.30), residues: 281 loop : -0.81 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 314 TYR 0.027 0.002 TYR H 235 PHE 0.015 0.002 PHE C 199 TRP 0.011 0.002 TRP C 82 HIS 0.004 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 9440) covalent geometry : angle 0.63853 / 0.33 (12799) SS BOND : bond 0.00558 / 0.37 ( 3) SS BOND : angle 2.15669 / 1.28 ( 6) hydrogen bonds : bond 0.04961 / 3.63 ( 449) hydrogen bonds : angle 4.49130 / 3.43 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5763 (ttp) cc_final: 0.5487 (ttm) REVERT: A 216 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7085 (tt) REVERT: A 286 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6371 (t80) REVERT: A 298 MET cc_start: 0.6281 (tpp) cc_final: 0.5933 (tpt) REVERT: B 15 ASP cc_start: 0.7400 (m-30) cc_final: 0.7099 (m-30) REVERT: B 60 ARG cc_start: 0.7113 (ttp80) cc_final: 0.5803 (mmp-170) REVERT: B 202 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6528 (ptm160) REVERT: B 261 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.6680 (m-80) REVERT: B 280 GLU cc_start: 0.7961 (tp30) cc_final: 0.7423 (tm-30) REVERT: B 322 LYS cc_start: 0.7671 (mtpp) cc_final: 0.6935 (tptt) REVERT: C 52 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7620 (mtp85) REVERT: C 76 ASP cc_start: 0.7424 (p0) cc_final: 0.7036 (p0) REVERT: C 129 ARG cc_start: 0.7394 (mtt180) cc_final: 0.7170 (ttt90) REVERT: C 188 MET cc_start: 0.7233 (mmm) cc_final: 0.7010 (mmp) REVERT: C 269 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6770 (mm) REVERT: H 235 TYR cc_start: 0.4763 (OUTLIER) cc_final: 0.4333 (t80) outliers start: 53 outliers final: 31 residues processed: 161 average time/residue: 0.6460 time to fit residues: 110.1648 Evaluate side-chains 150 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 286 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 115 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 0.0050 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN B 357 ASN H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.209320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.170035 restraints weight = 9573.919| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 1.94 r_work: 0.3983 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9443 Z= 0.118 Angle : 0.577 8.265 12805 Z= 0.299 Chirality : 0.042 0.228 1439 Planarity : 0.004 0.043 1630 Dihedral : 5.113 54.508 1299 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.35 % Allowed : 19.41 % Favored : 76.24 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 1.02 (0.25), residues: 1162 helix: 2.34 (0.25), residues: 414 sheet: 0.57 (0.31), residues: 275 loop : -0.77 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 38 TYR 0.026 0.001 TYR B 285 PHE 0.014 0.001 PHE C 199 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9440) covalent geometry : angle 0.57631 / 0.30 (12799) SS BOND : bond 0.00423 / 0.28 ( 3) SS BOND : angle 1.53733 / 0.95 ( 6) hydrogen bonds : bond 0.04046 / 2.96 ( 449) hydrogen bonds : angle 4.25203 / 3.25 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5742 (ttp) cc_final: 0.5483 (ttm) REVERT: A 216 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7128 (tt) REVERT: B 38 ARG cc_start: 0.7218 (mtp-110) cc_final: 0.6920 (mtp85) REVERT: B 60 ARG cc_start: 0.7042 (ttp80) cc_final: 0.5648 (mmp-170) REVERT: B 202 ARG cc_start: 0.6995 (mtp85) cc_final: 0.6503 (ptm160) REVERT: B 261 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6427 (m-80) REVERT: B 280 GLU cc_start: 0.7898 (tp30) cc_final: 0.7239 (tm-30) REVERT: B 281 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: B 322 LYS cc_start: 0.7696 (mtpp) cc_final: 0.6968 (tptt) REVERT: B 335 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6629 (tp30) REVERT: C 52 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7609 (mtp85) REVERT: C 76 ASP cc_start: 0.7290 (p0) cc_final: 0.6924 (p0) REVERT: C 101 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7322 (mtp) REVERT: C 129 ARG cc_start: 0.7365 (mtt180) cc_final: 0.7153 (ttt90) REVERT: C 188 MET cc_start: 0.7124 (mmm) cc_final: 0.6860 (mmp) REVERT: C 234 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: C 269 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6707 (mm) REVERT: H 186 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7528 (pp30) REVERT: H 235 TYR cc_start: 0.4537 (OUTLIER) cc_final: 0.4148 (t80) REVERT: H 244 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7854 (ttpp) outliers start: 43 outliers final: 22 residues processed: 155 average time/residue: 0.5954 time to fit residues: 97.8097 Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.207061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.171494 restraints weight = 9699.950| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.77 r_work: 0.3943 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9443 Z= 0.142 Angle : 0.605 8.394 12805 Z= 0.312 Chirality : 0.042 0.244 1439 Planarity : 0.004 0.042 1630 Dihedral : 5.036 53.661 1299 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.65 % Allowed : 20.12 % Favored : 75.23 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.96 (0.25), residues: 1162 helix: 2.27 (0.25), residues: 413 sheet: 0.46 (0.31), residues: 282 loop : -0.75 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 147 TYR 0.025 0.001 TYR H 235 PHE 0.014 0.002 PHE C 199 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9440) covalent geometry : angle 0.60409 / 0.31 (12799) SS BOND : bond 0.00433 / 0.29 ( 3) SS BOND : angle 1.65727 / 1.03 ( 6) hydrogen bonds : bond 0.04424 / 3.23 ( 449) hydrogen bonds : angle 4.26182 / 3.25 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 125 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5777 (ttp) cc_final: 0.5509 (ttm) REVERT: A 216 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7175 (tt) REVERT: A 298 MET cc_start: 0.6042 (tpp) cc_final: 0.5622 (tpt) REVERT: B 60 ARG cc_start: 0.7120 (ttp80) cc_final: 0.5746 (mmp-170) REVERT: B 147 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7143 (pmt170) REVERT: B 202 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6464 (ptm160) REVERT: B 261 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: B 280 GLU cc_start: 0.7905 (tp30) cc_final: 0.7257 (tm-30) REVERT: B 281 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: B 322 LYS cc_start: 0.7781 (mtpp) cc_final: 0.6961 (tptt) REVERT: B 335 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6585 (tp30) REVERT: C 52 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7613 (mtp85) REVERT: C 101 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7386 (mtp) REVERT: C 129 ARG cc_start: 0.7400 (mtt180) cc_final: 0.7150 (ttt90) REVERT: C 188 MET cc_start: 0.7153 (mmm) cc_final: 0.6917 (mmp) REVERT: C 234 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: C 269 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6750 (mm) REVERT: H 235 TYR cc_start: 0.4681 (OUTLIER) cc_final: 0.4226 (t80) REVERT: H 244 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7816 (tmtm) outliers start: 46 outliers final: 29 residues processed: 157 average time/residue: 0.6198 time to fit residues: 103.0078 Evaluate side-chains 156 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 0.0010 chunk 89 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN H 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.208262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.171812 restraints weight = 9710.889| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.71 r_work: 0.3972 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3834 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9443 Z= 0.121 Angle : 0.579 8.254 12805 Z= 0.298 Chirality : 0.041 0.227 1439 Planarity : 0.004 0.047 1630 Dihedral : 4.889 52.985 1299 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.65 % Allowed : 20.53 % Favored : 74.82 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 1.06 (0.25), residues: 1162 helix: 2.36 (0.25), residues: 414 sheet: 0.61 (0.31), residues: 277 loop : -0.75 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 38 TYR 0.026 0.001 TYR B 285 PHE 0.018 0.001 PHE A 329 TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9440) covalent geometry : angle 0.57822 / 0.30 (12799) SS BOND : bond 0.00397 / 0.27 ( 3) SS BOND : angle 1.45445 / 0.91 ( 6) hydrogen bonds : bond 0.04058 / 2.97 ( 449) hydrogen bonds : angle 4.16465 / 3.18 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5905 (ttp) cc_final: 0.5604 (ttm) REVERT: A 216 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7281 (tt) REVERT: A 298 MET cc_start: 0.6071 (tpp) cc_final: 0.5710 (tpt) REVERT: B 38 ARG cc_start: 0.7143 (mtp-110) cc_final: 0.6816 (mtp85) REVERT: B 39 GLU cc_start: 0.6371 (tp30) cc_final: 0.6146 (tp30) REVERT: B 60 ARG cc_start: 0.7139 (ttp80) cc_final: 0.5753 (mmp-170) REVERT: B 147 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.7181 (pmt170) REVERT: B 202 ARG cc_start: 0.7065 (mtp85) cc_final: 0.6588 (ptm160) REVERT: B 261 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6497 (m-80) REVERT: B 280 GLU cc_start: 0.7959 (tp30) cc_final: 0.7338 (tm-30) REVERT: B 281 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: B 322 LYS cc_start: 0.7734 (mtpp) cc_final: 0.6994 (tptt) REVERT: B 333 ASP cc_start: 0.6367 (m-30) cc_final: 0.5840 (m-30) REVERT: B 335 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6672 (tp30) REVERT: C 52 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7618 (mtp85) REVERT: C 76 ASP cc_start: 0.7241 (p0) cc_final: 0.6959 (p0) REVERT: C 101 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7322 (mtp) REVERT: C 129 ARG cc_start: 0.7450 (mtt180) cc_final: 0.7242 (ttt90) REVERT: C 188 MET cc_start: 0.7097 (mmm) cc_final: 0.6852 (mmp) REVERT: C 234 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: C 269 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6791 (mm) REVERT: D 52 THR cc_start: 0.6181 (t) cc_final: 0.5828 (m) REVERT: H 67 ARG cc_start: 0.5169 (ptt90) cc_final: 0.4778 (ptt90) REVERT: H 186 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7570 (pp30) REVERT: H 235 TYR cc_start: 0.4557 (OUTLIER) cc_final: 0.4148 (t80) REVERT: H 244 LYS cc_start: 0.8332 (ttpp) cc_final: 0.7893 (tmtm) outliers start: 46 outliers final: 29 residues processed: 161 average time/residue: 0.5496 time to fit residues: 94.1375 Evaluate side-chains 158 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.0050 chunk 5 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.209855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.173796 restraints weight = 9583.715| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.70 r_work: 0.3983 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9443 Z= 0.115 Angle : 0.579 9.820 12805 Z= 0.296 Chirality : 0.041 0.222 1439 Planarity : 0.004 0.044 1630 Dihedral : 4.645 52.618 1297 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.74 % Allowed : 21.33 % Favored : 74.92 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 1.10 (0.25), residues: 1162 helix: 2.40 (0.26), residues: 413 sheet: 0.67 (0.31), residues: 277 loop : -0.76 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 38 TYR 0.022 0.001 TYR H 235 PHE 0.012 0.001 PHE C 199 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9440) covalent geometry : angle 0.57820 / 0.30 (12799) SS BOND : bond 0.00390 / 0.26 ( 3) SS BOND : angle 1.42851 / 0.92 ( 6) hydrogen bonds : bond 0.03847 / 2.82 ( 449) hydrogen bonds : angle 4.13285 / 3.16 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5915 (ttp) cc_final: 0.5627 (ttm) REVERT: A 216 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7261 (tt) REVERT: A 298 MET cc_start: 0.6105 (tpp) cc_final: 0.5769 (tpt) REVERT: B 38 ARG cc_start: 0.7148 (mtp-110) cc_final: 0.6796 (mtp85) REVERT: B 39 GLU cc_start: 0.6352 (tp30) cc_final: 0.6114 (tp30) REVERT: B 60 ARG cc_start: 0.7154 (ttp80) cc_final: 0.5787 (mmp-170) REVERT: B 147 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.7159 (pmt170) REVERT: B 202 ARG cc_start: 0.7107 (mtp85) cc_final: 0.6596 (ptm160) REVERT: B 261 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: B 280 GLU cc_start: 0.7975 (tp30) cc_final: 0.7350 (tm-30) REVERT: B 281 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: B 333 ASP cc_start: 0.6434 (m-30) cc_final: 0.5917 (m-30) REVERT: B 335 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6649 (tp30) REVERT: C 52 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7615 (mtp85) REVERT: C 101 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7301 (mtp) REVERT: C 175 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7864 (mm-40) REVERT: C 188 MET cc_start: 0.7108 (mmm) cc_final: 0.6828 (mmp) REVERT: C 234 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: C 269 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6759 (mm) REVERT: D 52 THR cc_start: 0.6229 (t) cc_final: 0.5918 (m) REVERT: H 67 ARG cc_start: 0.5156 (ptt90) cc_final: 0.4756 (ptt90) REVERT: H 235 TYR cc_start: 0.4566 (OUTLIER) cc_final: 0.4155 (t80) REVERT: H 244 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7868 (tmtm) outliers start: 37 outliers final: 28 residues processed: 154 average time/residue: 0.5610 time to fit residues: 91.5447 Evaluate side-chains 155 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.207914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.171050 restraints weight = 9611.793| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.73 r_work: 0.3954 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9443 Z= 0.134 Angle : 0.602 8.795 12805 Z= 0.310 Chirality : 0.042 0.232 1439 Planarity : 0.004 0.042 1630 Dihedral : 4.699 52.664 1297 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.04 % Allowed : 21.33 % Favored : 74.62 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 1.02 (0.25), residues: 1162 helix: 2.28 (0.25), residues: 413 sheet: 0.66 (0.32), residues: 278 loop : -0.79 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 38 TYR 0.027 0.001 TYR B 285 PHE 0.031 0.002 PHE A 329 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9440) covalent geometry : angle 0.60163 / 0.31 (12799) SS BOND : bond 0.00415 / 0.28 ( 3) SS BOND : angle 1.51893 / 0.97 ( 6) hydrogen bonds : bond 0.04182 / 3.06 ( 449) hydrogen bonds : angle 4.20955 / 3.22 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5902 (ttp) cc_final: 0.5612 (ttm) REVERT: A 298 MET cc_start: 0.6135 (tpp) cc_final: 0.5816 (tpt) REVERT: B 31 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7227 (tm-30) REVERT: B 38 ARG cc_start: 0.7201 (mtp-110) cc_final: 0.6864 (mtp85) REVERT: B 39 GLU cc_start: 0.6388 (tp30) cc_final: 0.6124 (tp30) REVERT: B 60 ARG cc_start: 0.7188 (ttp80) cc_final: 0.5794 (mmp-170) REVERT: B 147 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7197 (pmt170) REVERT: B 160 TYR cc_start: 0.5876 (m-10) cc_final: 0.5213 (m-10) REVERT: B 202 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6586 (ptm160) REVERT: B 261 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7255 (m-10) REVERT: B 280 GLU cc_start: 0.7984 (tp30) cc_final: 0.7320 (tm-30) REVERT: B 281 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: B 333 ASP cc_start: 0.6347 (m-30) cc_final: 0.5874 (m-30) REVERT: B 335 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: C 52 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7558 (mtp85) REVERT: C 101 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7382 (mtp) REVERT: C 175 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7859 (mm-40) REVERT: C 188 MET cc_start: 0.7096 (mmm) cc_final: 0.6870 (mmp) REVERT: C 234 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6883 (m-80) REVERT: C 269 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6793 (mm) REVERT: D 52 THR cc_start: 0.6155 (t) cc_final: 0.5813 (m) REVERT: H 67 ARG cc_start: 0.5121 (ptt90) cc_final: 0.4771 (ptt90) REVERT: H 235 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.4144 (t80) outliers start: 40 outliers final: 25 residues processed: 153 average time/residue: 0.5486 time to fit residues: 89.1575 Evaluate side-chains 152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.204499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.166516 restraints weight = 9692.808| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.82 r_work: 0.3904 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9443 Z= 0.175 Angle : 0.666 11.178 12805 Z= 0.341 Chirality : 0.044 0.254 1439 Planarity : 0.005 0.042 1630 Dihedral : 4.942 52.837 1297 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.94 % Allowed : 21.33 % Favored : 74.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 0.87 (0.25), residues: 1162 helix: 2.02 (0.25), residues: 413 sheet: 0.63 (0.32), residues: 276 loop : -0.75 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 68 TYR 0.026 0.002 TYR H 235 PHE 0.016 0.002 PHE B 201 TRP 0.012 0.002 TRP C 82 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 9440) covalent geometry : angle 0.66508 / 0.34 (12799) SS BOND : bond 0.00475 / 0.32 ( 3) SS BOND : angle 1.69410 / 1.08 ( 6) hydrogen bonds : bond 0.04850 / 3.55 ( 449) hydrogen bonds : angle 4.41654 / 3.38 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5811 (ttp) cc_final: 0.5546 (ttm) REVERT: B 15 ASP cc_start: 0.7532 (m-30) cc_final: 0.7254 (m-30) REVERT: B 38 ARG cc_start: 0.7258 (mtp-110) cc_final: 0.6906 (mtp85) REVERT: B 39 GLU cc_start: 0.6305 (tp30) cc_final: 0.6094 (tp30) REVERT: B 60 ARG cc_start: 0.7212 (ttp80) cc_final: 0.5808 (mmp-170) REVERT: B 147 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7177 (pmt170) REVERT: B 160 TYR cc_start: 0.5772 (m-10) cc_final: 0.5172 (m-10) REVERT: B 202 ARG cc_start: 0.7150 (mtp85) cc_final: 0.6556 (ptm160) REVERT: B 261 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6583 (m-80) REVERT: B 280 GLU cc_start: 0.7949 (tp30) cc_final: 0.7241 (tm-30) REVERT: B 281 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6286 (mp0) REVERT: B 333 ASP cc_start: 0.6338 (m-30) cc_final: 0.5899 (m-30) REVERT: B 335 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6690 (tp30) REVERT: C 52 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7573 (mtp85) REVERT: C 101 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7397 (mtp) REVERT: C 153 ASP cc_start: 0.7068 (m-30) cc_final: 0.6856 (m-30) REVERT: C 175 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7861 (mm-40) REVERT: C 188 MET cc_start: 0.7156 (mmm) cc_final: 0.6950 (mmp) REVERT: C 234 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: C 269 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6814 (mm) REVERT: H 235 TYR cc_start: 0.4785 (OUTLIER) cc_final: 0.4325 (t80) REVERT: H 244 LYS cc_start: 0.8209 (ttpp) cc_final: 0.7831 (ttpp) outliers start: 39 outliers final: 30 residues processed: 149 average time/residue: 0.6113 time to fit residues: 96.5547 Evaluate side-chains 153 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 113 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 148 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 137 ARG Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 52 optimal weight: 0.0980 chunk 25 optimal weight: 0.0030 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.209401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.167629 restraints weight = 9499.150| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.00 r_work: 0.3960 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9443 Z= 0.117 Angle : 0.608 9.001 12805 Z= 0.310 Chirality : 0.042 0.220 1439 Planarity : 0.004 0.042 1630 Dihedral : 4.776 51.731 1297 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.44 % Allowed : 22.14 % Favored : 74.42 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: 1.06 (0.25), residues: 1162 helix: 2.29 (0.26), residues: 412 sheet: 0.78 (0.32), residues: 269 loop : -0.76 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.027 0.001 TYR B 285 PHE 0.027 0.001 PHE A 329 TRP 0.020 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 9440) covalent geometry : angle 0.60734 / 0.31 (12799) SS BOND : bond 0.00462 / 0.31 ( 3) SS BOND : angle 1.42654 / 0.96 ( 6) hydrogen bonds : bond 0.03904 / 2.87 ( 449) hydrogen bonds : angle 4.23750 / 3.24 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5330.76 seconds wall clock time: 91 minutes 2.32 seconds (5462.32 seconds total)