Starting phenix.real_space_refine on Tue Mar 3 23:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w40_32298/03_2026/7w40_32298.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w40_32298/03_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_32298/03_2026/7w40_32298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w40_32298/03_2026/7w40_32298.map" model { file = "/net/cci-nas-00/data/ceres_data/7w40_32298/03_2026/7w40_32298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w40_32298/03_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-5986/lib/python3.9/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} Modifications used: {'PEPT-D': 1} Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BAL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.08, per 1000 atoms: 0.23 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: 0.67 Conformation dependent library (CDL) restraints added in 267.1 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: 0.30 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: 1.11 Time building geometry restraints manager: 0.86 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 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=" CB DPN E 1 " pdb=" CG DPN E 1 " ideal model delta sigma weight residual 1.502 1.391 0.111 2.30e-02 1.89e+03 2.34e+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: 405 33.46 - 50.20: 78 50.20 - 66.93: 15 66.93 - 83.66: 2 Dihedral angle restraints: 5602 sinusoidal: 2154 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 5599 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: 0.970 Set stop_for_unknowns flag: 0.010 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.830 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: 0.010 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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= 0.716 Angle : 1.290 8.202 12805 Z= 0.929 Chirality : 0.085 0.675 1439 Planarity : 0.006 0.053 1630 Dihedral : 12.467 83.658 3371 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 covalent geometry : bond 0.01062 ( 9440) covalent geometry : angle 1.28847 (12799) SS BOND : bond 0.02111 ( 3) SS BOND : angle 3.05823 ( 6) hydrogen bonds : bond 0.17159 ( 449) hydrogen bonds : angle 6.82059 ( 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 : 0.355 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: 0.5616 time to fit residues: 147.0928 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 : 0.326 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4530 r_free = 0.4530 target = 0.212379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.173685 restraints weight = 9644.218| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.21 r_work: 0.3989 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9443 Z= 0.144 Angle : 0.644 9.720 12805 Z= 0.336 Chirality : 0.043 0.285 1439 Planarity : 0.005 0.049 1630 Dihedral : 5.391 46.198 1303 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.55 % Allowed : 13.35 % 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: 0.58 (0.24), residues: 1162 helix: 1.76 (0.24), residues: 418 sheet: 0.46 (0.30), residues: 289 loop : -0.95 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.048 0.002 TYR H 235 PHE 0.016 0.002 PHE B 201 TRP 0.022 0.001 TRP C 82 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9440) covalent geometry : angle 0.64350 (12799) SS BOND : bond 0.00344 ( 3) SS BOND : angle 1.20763 ( 6) hydrogen bonds : bond 0.04943 ( 449) hydrogen bonds : angle 4.71563 ( 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 197 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7753 (mptt) cc_final: 0.7213 (mttp) REVERT: B 38 ARG cc_start: 0.7602 (mtp-110) cc_final: 0.7261 (mtp85) REVERT: B 60 ARG cc_start: 0.7038 (ttp80) cc_final: 0.5567 (mmp-170) REVERT: B 202 ARG cc_start: 0.7040 (mtp85) cc_final: 0.6438 (ptm160) REVERT: B 303 GLN cc_start: 0.6586 (tp40) cc_final: 0.6157 (tp40) REVERT: B 322 LYS cc_start: 0.7643 (mtpp) cc_final: 0.6884 (tptt) REVERT: C 76 ASP cc_start: 0.7057 (p0) cc_final: 0.5900 (t0) REVERT: C 129 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6733 (ttt90) REVERT: C 188 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6930 (mmp) REVERT: C 197 ARG cc_start: 0.6887 (mtp85) cc_final: 0.6513 (mmt180) REVERT: H 244 LYS cc_start: 0.8053 (tttt) cc_final: 0.7809 (ttpp) outliers start: 45 outliers final: 18 residues processed: 180 average time/residue: 0.6530 time to fit residues: 124.1626 Evaluate side-chains 142 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET 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 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 188 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 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: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN C 142 HIS H 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.206900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.170253 restraints weight = 9602.599| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.75 r_work: 0.3951 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9443 Z= 0.164 Angle : 0.637 8.451 12805 Z= 0.335 Chirality : 0.044 0.261 1439 Planarity : 0.004 0.045 1630 Dihedral : 5.720 74.083 1303 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.06 % Allowed : 16.08 % Favored : 78.87 % 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: 2.09 (0.25), residues: 412 sheet: 0.43 (0.31), residues: 280 loop : -0.87 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 314 TYR 0.026 0.002 TYR H 235 PHE 0.018 0.002 PHE C 253 TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9440) covalent geometry : angle 0.63426 (12799) SS BOND : bond 0.00997 ( 3) SS BOND : angle 2.85307 ( 6) hydrogen bonds : bond 0.05125 ( 449) hydrogen bonds : angle 4.57488 ( 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 182 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 286 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.6374 (t80) REVERT: B 60 ARG cc_start: 0.7134 (ttp80) cc_final: 0.5734 (mmp-170) REVERT: B 202 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6621 (ptm160) REVERT: B 280 GLU cc_start: 0.8001 (tp30) cc_final: 0.7555 (tm-30) REVERT: B 322 LYS cc_start: 0.7628 (mtpp) cc_final: 0.6867 (tptt) REVERT: B 335 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6718 (tp30) REVERT: C 52 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7572 (mtp85) REVERT: C 76 ASP cc_start: 0.7443 (p0) cc_final: 0.7058 (p0) REVERT: C 129 ARG cc_start: 0.7275 (mtt180) cc_final: 0.7056 (ttt90) REVERT: C 188 MET cc_start: 0.7197 (mmm) cc_final: 0.6953 (mmp) REVERT: C 197 ARG cc_start: 0.6994 (mtp85) cc_final: 0.6601 (mmp80) REVERT: C 269 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6662 (mm) REVERT: H 235 TYR cc_start: 0.4583 (OUTLIER) cc_final: 0.4165 (t80) REVERT: H 244 LYS cc_start: 0.8255 (tttt) cc_final: 0.8053 (ttpp) outliers start: 50 outliers final: 26 residues processed: 168 average time/residue: 0.6518 time to fit residues: 115.9577 Evaluate side-chains 147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 148 ARG Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 335 GLU 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 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 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 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: 0.7980 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 0.0070 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.207252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.167223 restraints weight = 9723.171| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 1.97 r_work: 0.3952 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9443 Z= 0.145 Angle : 0.617 7.863 12805 Z= 0.318 Chirality : 0.043 0.252 1439 Planarity : 0.004 0.043 1630 Dihedral : 5.451 65.358 1301 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.75 % Allowed : 17.80 % Favored : 77.45 % 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: 0.89 (0.24), residues: 1162 helix: 2.20 (0.25), residues: 413 sheet: 0.51 (0.31), residues: 275 loop : -0.82 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 38 TYR 0.026 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 covalent geometry : bond 0.00330 ( 9440) covalent geometry : angle 0.61532 (12799) SS BOND : bond 0.00453 ( 3) SS BOND : angle 2.09581 ( 6) hydrogen bonds : bond 0.04610 ( 449) hydrogen bonds : angle 4.39377 ( 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 171 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5897 (ttp) cc_final: 0.5628 (ttm) REVERT: A 286 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.6300 (t80) REVERT: A 298 MET cc_start: 0.6223 (tpp) cc_final: 0.5907 (tpt) REVERT: B 38 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7047 (mtp85) REVERT: B 60 ARG cc_start: 0.7089 (ttp80) cc_final: 0.5701 (mmp-170) REVERT: B 202 ARG cc_start: 0.7093 (mtp85) cc_final: 0.6533 (ptm160) REVERT: B 261 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: B 280 GLU cc_start: 0.7948 (tp30) cc_final: 0.7506 (tm-30) REVERT: B 322 LYS cc_start: 0.7721 (mtpp) cc_final: 0.6961 (tptt) REVERT: C 52 ARG cc_start: 0.7890 (mtt90) cc_final: 0.7626 (mtp85) REVERT: C 76 ASP cc_start: 0.7368 (p0) cc_final: 0.6923 (p0) REVERT: C 101 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7452 (mtp) REVERT: C 129 ARG cc_start: 0.7330 (mtt180) cc_final: 0.7104 (ttt90) REVERT: C 188 MET cc_start: 0.7177 (mmm) cc_final: 0.6943 (mmp) REVERT: C 197 ARG cc_start: 0.6950 (mtp85) cc_final: 0.6685 (mmt180) REVERT: C 269 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6683 (mm) REVERT: H 235 TYR cc_start: 0.4705 (OUTLIER) cc_final: 0.4262 (t80) REVERT: H 244 LYS cc_start: 0.8221 (tttt) cc_final: 0.8007 (ttpp) REVERT: H 246 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5491 (pt0) outliers start: 47 outliers final: 26 residues processed: 152 average time/residue: 0.6647 time to fit residues: 106.7822 Evaluate side-chains 146 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 199 TYR 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 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 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 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 H residue 246 GLU 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: 0.9980 chunk 25 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 ASN H 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.205328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.168590 restraints weight = 9633.084| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.73 r_work: 0.3931 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3835 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= 0.139 Angle : 0.591 7.809 12805 Z= 0.308 Chirality : 0.042 0.244 1439 Planarity : 0.004 0.042 1630 Dihedral : 5.263 54.006 1301 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.36 % Allowed : 18.40 % 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: 0.91 (0.24), residues: 1162 helix: 2.21 (0.25), residues: 412 sheet: 0.44 (0.31), residues: 279 loop : -0.74 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 314 TYR 0.025 0.002 TYR B 285 PHE 0.014 0.002 PHE C 199 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9440) covalent geometry : angle 0.59007 (12799) SS BOND : bond 0.00470 ( 3) SS BOND : angle 1.72803 ( 6) hydrogen bonds : bond 0.04522 ( 449) hydrogen bonds : angle 4.32235 ( 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 177 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5878 (ttp) cc_final: 0.5621 (ttm) REVERT: B 60 ARG cc_start: 0.7121 (ttp80) cc_final: 0.5769 (mmp-170) REVERT: B 202 ARG cc_start: 0.7094 (mtp85) cc_final: 0.6539 (ptm160) REVERT: B 261 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: B 280 GLU cc_start: 0.7894 (tp30) cc_final: 0.7308 (tm-30) REVERT: B 322 LYS cc_start: 0.7741 (mtpp) cc_final: 0.6968 (tptt) REVERT: B 335 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6662 (tp30) REVERT: C 52 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7615 (mtp85) REVERT: C 76 ASP cc_start: 0.7466 (p0) cc_final: 0.7030 (p0) REVERT: C 101 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7449 (mtp) REVERT: C 188 MET cc_start: 0.7151 (mmm) cc_final: 0.6913 (mmp) REVERT: C 234 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: C 269 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6587 (mm) REVERT: H 67 ARG cc_start: 0.4941 (ptt180) cc_final: 0.4690 (ptt90) REVERT: H 186 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7505 (pp30) REVERT: H 235 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.4295 (t80) REVERT: H 246 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5412 (pt0) outliers start: 53 outliers final: 32 residues processed: 159 average time/residue: 0.6783 time to fit residues: 114.0444 Evaluate side-chains 154 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 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 137 ARG Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 196 THR 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 7 SER 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 215 THR Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain H residue 246 GLU 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: 0.0170 chunk 0 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.205243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.168704 restraints weight = 9730.002| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 1.74 r_work: 0.3919 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9443 Z= 0.155 Angle : 0.630 8.500 12805 Z= 0.324 Chirality : 0.043 0.250 1439 Planarity : 0.005 0.048 1630 Dihedral : 5.230 53.555 1301 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.85 % Allowed : 20.42 % 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: 0.85 (0.24), residues: 1162 helix: 2.12 (0.25), residues: 413 sheet: 0.46 (0.31), residues: 276 loop : -0.77 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 38 TYR 0.025 0.001 TYR H 235 PHE 0.016 0.002 PHE C 199 TRP 0.012 0.001 TRP C 82 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9440) covalent geometry : angle 0.62916 (12799) SS BOND : bond 0.00462 ( 3) SS BOND : angle 1.76354 ( 6) hydrogen bonds : bond 0.04681 ( 449) hydrogen bonds : angle 4.33828 ( 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 169 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 121 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5917 (ttp) cc_final: 0.5641 (ttm) REVERT: A 298 MET cc_start: 0.5845 (tpp) cc_final: 0.5438 (tpt) REVERT: B 15 ASP cc_start: 0.7470 (m-30) cc_final: 0.7188 (m-30) REVERT: B 38 ARG cc_start: 0.7334 (mtp-110) cc_final: 0.7016 (mtp85) REVERT: B 60 ARG cc_start: 0.7174 (ttp80) cc_final: 0.5801 (mmp-170) REVERT: B 147 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7198 (pmt170) REVERT: B 202 ARG cc_start: 0.7052 (mtp85) cc_final: 0.6478 (ptm160) REVERT: B 261 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: B 280 GLU cc_start: 0.7924 (tp30) cc_final: 0.7263 (tm-30) REVERT: B 281 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: B 322 LYS cc_start: 0.7716 (mtpp) cc_final: 0.6957 (tptt) REVERT: B 335 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: C 52 ARG cc_start: 0.7875 (mtt90) cc_final: 0.7610 (mtp85) REVERT: C 76 ASP cc_start: 0.7487 (p0) cc_final: 0.7069 (p0) REVERT: C 101 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7437 (mtp) REVERT: C 175 GLN cc_start: 0.8236 (mm-40) cc_final: 0.8013 (mm-40) REVERT: C 188 MET cc_start: 0.7152 (mmm) cc_final: 0.6932 (mmp) REVERT: C 234 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6821 (m-80) REVERT: C 269 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6616 (mm) REVERT: H 67 ARG cc_start: 0.5008 (ptt180) cc_final: 0.4744 (ptt90) REVERT: H 235 TYR cc_start: 0.4720 (OUTLIER) cc_final: 0.4266 (t80) REVERT: H 244 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8013 (ttpp) outliers start: 48 outliers final: 30 residues processed: 154 average time/residue: 0.6344 time to fit residues: 103.4794 Evaluate side-chains 159 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 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 189 ILE 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 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 215 THR 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: 1.9990 chunk 33 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 0.0020 chunk 83 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 89 optimal weight: 0.3980 chunk 51 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 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 = 0.4511 r_free = 0.4511 target = 0.210091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.171679 restraints weight = 9755.469| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.91 r_work: 0.3989 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9443 Z= 0.108 Angle : 0.565 8.164 12805 Z= 0.290 Chirality : 0.041 0.213 1439 Planarity : 0.004 0.042 1630 Dihedral : 4.866 52.175 1301 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.25 % Allowed : 21.03 % 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: 1.11 (0.25), residues: 1162 helix: 2.40 (0.25), residues: 414 sheet: 0.64 (0.31), residues: 277 loop : -0.74 (0.28), 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 0.020 0.001 PHE A 329 TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9440) covalent geometry : angle 0.56421 (12799) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.34179 ( 6) hydrogen bonds : bond 0.03672 ( 449) hydrogen bonds : angle 4.10226 ( 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 174 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5866 (ttp) cc_final: 0.5608 (ttm) REVERT: A 298 MET cc_start: 0.6079 (tpp) cc_final: 0.5789 (tpt) REVERT: B 60 ARG cc_start: 0.7138 (ttp80) cc_final: 0.5788 (mmp-170) REVERT: B 147 ARG cc_start: 0.7452 (ttm-80) cc_final: 0.7131 (pmt170) REVERT: B 202 ARG cc_start: 0.7048 (mtp85) cc_final: 0.6552 (ptm160) REVERT: B 261 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.7347 (m-10) REVERT: B 280 GLU cc_start: 0.7992 (tp30) cc_final: 0.7388 (tm-30) REVERT: B 281 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: B 335 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6587 (tp30) REVERT: C 52 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7565 (mtp85) REVERT: C 76 ASP cc_start: 0.7212 (p0) cc_final: 0.6702 (p0) REVERT: C 101 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7348 (mtp) REVERT: C 175 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7915 (mm-40) REVERT: C 188 MET cc_start: 0.7133 (mmm) cc_final: 0.6867 (mmp) REVERT: C 234 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: D 21 MET cc_start: 0.6585 (tpp) cc_final: 0.6309 (mmm) REVERT: D 52 THR cc_start: 0.6064 (t) cc_final: 0.5749 (m) REVERT: H 67 ARG cc_start: 0.4865 (ptt180) cc_final: 0.4596 (ptt90) REVERT: H 186 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7586 (pp30) REVERT: H 235 TYR cc_start: 0.4504 (OUTLIER) cc_final: 0.4115 (t80) REVERT: H 244 LYS cc_start: 0.8401 (ttpp) cc_final: 0.8047 (ttpp) outliers start: 42 outliers final: 19 residues processed: 162 average time/residue: 0.6719 time to fit residues: 115.1521 Evaluate side-chains 144 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 65 SER 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 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 271 CYS Chi-restraints excluded: chain C residue 317 CYS 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 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: 4.9990 chunk 5 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN C 220 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 = 0.4487 r_free = 0.4487 target = 0.207267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.171244 restraints weight = 9643.664| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.72 r_work: 0.3947 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9443 Z= 0.140 Angle : 0.607 8.562 12805 Z= 0.313 Chirality : 0.042 0.235 1439 Planarity : 0.005 0.058 1630 Dihedral : 4.738 52.613 1298 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.64 % Allowed : 22.95 % Favored : 73.41 % 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: 0.98 (0.25), residues: 1162 helix: 2.27 (0.25), residues: 413 sheet: 0.57 (0.31), residues: 279 loop : -0.78 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 38 TYR 0.023 0.001 TYR H 235 PHE 0.014 0.002 PHE C 199 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9440) covalent geometry : angle 0.60629 (12799) SS BOND : bond 0.00449 ( 3) SS BOND : angle 1.62646 ( 6) hydrogen bonds : bond 0.04229 ( 449) hydrogen bonds : angle 4.16777 ( 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 164 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ILE cc_start: 0.6332 (OUTLIER) cc_final: 0.6000 (tt) REVERT: A 155 MET cc_start: 0.5899 (ttp) cc_final: 0.5651 (ttm) REVERT: A 287 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.5953 (mtp180) REVERT: A 298 MET cc_start: 0.6170 (tpp) cc_final: 0.5849 (tpt) REVERT: B 38 ARG cc_start: 0.7197 (mtp-110) cc_final: 0.6864 (mtp85) REVERT: B 60 ARG cc_start: 0.7175 (ttp80) cc_final: 0.5793 (mmp-170) REVERT: B 147 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.7211 (pmt170) REVERT: B 202 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6566 (ptm160) REVERT: B 261 TYR cc_start: 0.7671 (OUTLIER) cc_final: 0.7309 (m-10) REVERT: B 280 GLU cc_start: 0.8007 (tp30) cc_final: 0.7336 (tm-30) REVERT: B 281 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6263 (mp0) REVERT: B 335 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6720 (tp30) REVERT: C 52 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7578 (mtp85) REVERT: C 101 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7384 (mtp) REVERT: C 175 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7953 (mm-40) REVERT: C 188 MET cc_start: 0.7193 (mmm) cc_final: 0.6913 (mmp) REVERT: C 234 PHE cc_start: 0.7717 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: D 52 THR cc_start: 0.6249 (t) cc_final: 0.5919 (m) REVERT: H 67 ARG cc_start: 0.4822 (OUTLIER) cc_final: 0.4571 (ptt90) REVERT: H 186 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7442 (pp30) REVERT: H 235 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.4296 (t80) REVERT: H 244 LYS cc_start: 0.8463 (ttpp) cc_final: 0.8189 (ttpp) outliers start: 36 outliers final: 22 residues processed: 154 average time/residue: 0.6781 time to fit residues: 110.4879 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 : 0.226 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain A residue 287 ARG 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 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 271 CYS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain H residue 67 ARG 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 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: 0.8980 chunk 85 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 336 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 = 0.4490 r_free = 0.4490 target = 0.207651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.166923 restraints weight = 9579.153| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.90 r_work: 0.3923 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4397 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= 0.141 Angle : 0.618 10.334 12805 Z= 0.317 Chirality : 0.042 0.238 1439 Planarity : 0.005 0.053 1630 Dihedral : 4.781 52.751 1298 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.84 % Allowed : 22.04 % Favored : 74.12 % 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: 0.97 (0.25), residues: 1162 helix: 2.25 (0.25), residues: 413 sheet: 0.58 (0.32), residues: 279 loop : -0.78 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 38 TYR 0.027 0.001 TYR B 285 PHE 0.030 0.002 PHE A 329 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9440) covalent geometry : angle 0.61719 (12799) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.65313 ( 6) hydrogen bonds : bond 0.04269 ( 449) hydrogen bonds : angle 4.21320 ( 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 164 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ILE cc_start: 0.6191 (OUTLIER) cc_final: 0.5862 (tt) REVERT: A 155 MET cc_start: 0.5876 (ttp) cc_final: 0.5611 (ttm) REVERT: A 287 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.5981 (mtp180) REVERT: A 298 MET cc_start: 0.6134 (tpp) cc_final: 0.5828 (tpt) REVERT: B 38 ARG cc_start: 0.7260 (mtp-110) cc_final: 0.6897 (mtp85) REVERT: B 60 ARG cc_start: 0.7135 (ttp80) cc_final: 0.5722 (mmp-170) REVERT: B 147 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7205 (pmt170) REVERT: B 202 ARG cc_start: 0.7066 (mtp85) cc_final: 0.6418 (ptm160) REVERT: B 261 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.7310 (m-10) REVERT: B 280 GLU cc_start: 0.7976 (tp30) cc_final: 0.7234 (tm-30) REVERT: B 281 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: B 335 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6640 (tp30) REVERT: C 52 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7585 (mtp85) REVERT: C 101 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7427 (mtp) REVERT: C 175 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7909 (mm-40) REVERT: C 234 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: C 269 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6706 (mm) REVERT: D 52 THR cc_start: 0.6105 (t) cc_final: 0.5770 (m) REVERT: H 67 ARG cc_start: 0.4834 (OUTLIER) cc_final: 0.4558 (ptt90) REVERT: H 186 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7598 (pp30) REVERT: H 235 TYR cc_start: 0.4625 (OUTLIER) cc_final: 0.4178 (t80) REVERT: H 244 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8097 (ttpp) outliers start: 38 outliers final: 22 residues processed: 150 average time/residue: 0.7072 time to fit residues: 111.9799 Evaluate side-chains 154 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain A residue 287 ARG 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 321 ASP Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain C residue 101 MET 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 H residue 67 ARG 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 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: 0.0370 chunk 34 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 0.0170 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 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 = 0.4503 r_free = 0.4503 target = 0.208942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.168101 restraints weight = 9621.399| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.96 r_work: 0.3954 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.4477 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= 0.119 Angle : 0.601 9.900 12805 Z= 0.307 Chirality : 0.042 0.225 1439 Planarity : 0.004 0.048 1630 Dihedral : 4.716 52.574 1298 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.34 % Allowed : 22.95 % Favored : 73.71 % 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: 1.05 (0.25), residues: 1162 helix: 2.34 (0.26), residues: 412 sheet: 0.71 (0.32), residues: 276 loop : -0.82 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 38 TYR 0.022 0.001 TYR H 235 PHE 0.013 0.001 PHE A 329 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9440) covalent geometry : angle 0.60071 (12799) SS BOND : bond 0.00466 ( 3) SS BOND : angle 1.54635 ( 6) hydrogen bonds : bond 0.03905 ( 449) hydrogen bonds : angle 4.16947 ( 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 157 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.5844 (ttp) cc_final: 0.5592 (ttm) REVERT: A 298 MET cc_start: 0.6158 (tpp) cc_final: 0.5856 (tpt) REVERT: B 38 ARG cc_start: 0.7184 (mtp-110) cc_final: 0.6864 (mtp85) REVERT: B 60 ARG cc_start: 0.7170 (ttp80) cc_final: 0.5757 (mmp-170) REVERT: B 147 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7008 (pmt170) REVERT: B 160 TYR cc_start: 0.5759 (m-10) cc_final: 0.5148 (m-10) REVERT: B 202 ARG cc_start: 0.6988 (mtp85) cc_final: 0.6349 (ptm160) REVERT: B 261 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.7325 (m-10) REVERT: B 280 GLU cc_start: 0.8008 (tp30) cc_final: 0.7350 (tm-30) REVERT: B 281 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6177 (mp0) REVERT: B 335 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6600 (tp30) REVERT: C 52 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7575 (mtp85) REVERT: C 101 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7369 (mtp) REVERT: C 175 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7879 (mm-40) REVERT: C 234 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: D 52 THR cc_start: 0.6026 (t) cc_final: 0.5724 (m) REVERT: H 67 ARG cc_start: 0.4723 (ptt180) cc_final: 0.4497 (ptt90) REVERT: H 186 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7502 (pp30) REVERT: H 235 TYR cc_start: 0.4628 (OUTLIER) cc_final: 0.4224 (t80) REVERT: H 244 LYS cc_start: 0.8427 (ttpp) cc_final: 0.8148 (ttpp) outliers start: 33 outliers final: 20 residues processed: 148 average time/residue: 0.6558 time to fit residues: 102.7824 Evaluate side-chains 144 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET 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 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 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 271 CYS Chi-restraints excluded: chain C residue 317 CYS 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 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN B 336 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 = 0.4496 r_free = 0.4496 target = 0.208114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.167257 restraints weight = 9481.046| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.95 r_work: 0.3939 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9443 Z= 0.136 Angle : 0.616 9.525 12805 Z= 0.315 Chirality : 0.042 0.231 1439 Planarity : 0.004 0.049 1630 Dihedral : 4.767 52.578 1298 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.24 % Allowed : 23.05 % Favored : 73.71 % 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: 1.05 (0.25), residues: 1162 helix: 2.28 (0.26), residues: 412 sheet: 0.83 (0.32), residues: 267 loop : -0.81 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 38 TYR 0.027 0.002 TYR B 285 PHE 0.023 0.001 PHE A 329 TRP 0.012 0.001 TRP C 82 HIS 0.007 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9440) covalent geometry : angle 0.61474 (12799) SS BOND : bond 0.00455 ( 3) SS BOND : angle 1.65206 ( 6) hydrogen bonds : bond 0.04118 ( 449) hydrogen bonds : angle 4.24045 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5667.68 seconds wall clock time: 96 minutes 34.26 seconds (5794.26 seconds total)