Starting phenix.real_space_refine on Wed Mar 12 23:48:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xav_33100/03_2025/7xav_33100.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xav_33100/03_2025/7xav_33100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xav_33100/03_2025/7xav_33100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xav_33100/03_2025/7xav_33100.map" model { file = "/net/cci-nas-00/data/ceres_data/7xav_33100/03_2025/7xav_33100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xav_33100/03_2025/7xav_33100.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.128 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 54 5.16 5 C 5319 2.51 5 N 1436 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1896 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1602 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 4.87, per 1000 atoms: 0.58 Number of scatterers: 8410 At special positions: 0 Unit cell: (87.74, 121.98, 127.33, 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 54 16.00 O 1601 8.00 N 1436 7.00 C 5319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 7 " 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 Links applied TRANS " DTR F 4 " - " TYR F 3 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 981.8 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTR F 4 " Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 30.2% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 43 through 61 removed outlier: 4.025A pdb=" N THR A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 77 through 92 removed outlier: 3.654A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.819A pdb=" N MET A 101 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 113 through 125 removed outlier: 4.776A pdb=" N MET A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 124 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.518A pdb=" N TYR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.622A pdb=" N SER A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 180 removed outlier: 3.657A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 219 through 236 removed outlier: 4.626A pdb=" N ILE A 231 " --> pdb=" O CYS A 227 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 4.061A pdb=" N LYS A 249 " --> pdb=" O LYS A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.626A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.639A pdb=" N SER A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.703A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 326 Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.758A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.641A pdb=" N LYS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.595A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.533A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.626A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.644A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.514A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.642A pdb=" N GLU C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.814A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.804A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.694A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.194A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.048A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.594A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.693A 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: 3.964A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.887A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.041A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.264A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.504A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.561A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.654A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.933A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 243 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.751A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 189 through 190 289 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 2.34 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: 2544 1.33 - 1.46: 2293 1.46 - 1.59: 3655 1.59 - 1.72: 0 1.72 - 1.85: 75 Bond restraints: 8567 Sorted by residual: bond pdb=" CB VAL C 112 " pdb=" CG2 VAL C 112 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 7.02e+00 bond pdb=" CG1 ILE C 338 " pdb=" CD1 ILE C 338 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.35e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.46e+00 bond pdb=" CA SER B 16 " pdb=" CB SER B 16 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.74e-02 3.30e+03 5.10e+00 bond pdb=" CB CYS C 317 " pdb=" SG CYS C 317 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.65e+00 ... (remaining 8562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 11490 3.53 - 7.07: 150 7.07 - 10.60: 19 10.60 - 14.14: 0 14.14 - 17.67: 1 Bond angle restraints: 11660 Sorted by residual: angle pdb=" C THR B 190 " pdb=" N PHE B 191 " pdb=" CA PHE B 191 " ideal model delta sigma weight residual 122.58 114.37 8.21 2.07e+00 2.33e-01 1.57e+01 angle pdb=" C ASP C 246 " pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 121.52 130.50 -8.98 2.34e+00 1.83e-01 1.47e+01 angle pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta sigma weight residual 125.66 132.54 -6.88 1.85e+00 2.92e-01 1.38e+01 angle pdb=" C ASN C 88 " pdb=" CA ASN C 88 " pdb=" CB ASN C 88 " ideal model delta sigma weight residual 109.38 115.72 -6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 ... (remaining 11655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 4441 15.39 - 30.77: 480 30.77 - 46.15: 118 46.15 - 61.54: 24 61.54 - 76.92: 7 Dihedral angle restraints: 5070 sinusoidal: 1769 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 161.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -31.70 -54.30 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sinusoidal sigma weight residual -86.00 -33.81 -52.19 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 5067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 911 0.054 - 0.108: 342 0.108 - 0.162: 90 0.162 - 0.216: 24 0.216 - 0.270: 9 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA CYS F 2 " pdb=" N CYS F 2 " pdb=" C CYS F 2 " pdb=" CB CYS F 2 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 145 " pdb=" CA VAL A 145 " pdb=" CG1 VAL A 145 " pdb=" CG2 VAL A 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1373 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO A 176 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 319 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ILE B 319 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE B 319 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR B 320 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " -0.029 2.00e-02 2.50e+03 1.99e-02 6.92e+00 pdb=" CG PHE C 151 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " -0.007 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.18: 1 2.18 - 2.86: 3112 2.86 - 3.54: 10857 3.54 - 4.22: 20826 4.22 - 4.90: 35098 Nonbonded interactions: 69894 Sorted by model distance: nonbonded pdb=" CG2 THR A 212 " pdb=" CZ3 DTR F 4 " model vdw 1.494 3.760 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.181 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.240 3.040 nonbonded pdb=" O ASP E 223 " pdb=" OH TYR E 227 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O GLY C 288 " model vdw 2.252 3.040 ... (remaining 69889 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.270 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.009 0.098 8567 Z= 0.614 Angle : 1.051 17.673 11660 Z= 0.567 Chirality : 0.064 0.270 1376 Planarity : 0.007 0.079 1489 Dihedral : 14.144 76.924 2920 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.71 % Allowed : 10.12 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.20), residues: 1120 helix: -4.55 (0.13), residues: 343 sheet: -1.92 (0.30), residues: 257 loop : -2.53 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 99 HIS 0.008 0.002 HIS C 91 PHE 0.042 0.004 PHE C 151 TYR 0.035 0.003 TYR C 105 ARG 0.006 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.898 Fit side-chains REVERT: A 122 ASP cc_start: 0.6663 (m-30) cc_final: 0.6403 (m-30) REVERT: A 173 VAL cc_start: 0.8208 (t) cc_final: 0.7973 (p) REVERT: A 180 TYR cc_start: 0.7658 (m-80) cc_final: 0.7038 (m-80) REVERT: A 196 ASN cc_start: 0.7340 (m110) cc_final: 0.7107 (m110) REVERT: B 24 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.7040 (ttp-110) REVERT: B 262 THR cc_start: 0.8514 (p) cc_final: 0.8314 (p) REVERT: B 333 GLN cc_start: 0.8052 (tp40) cc_final: 0.7360 (tp40) REVERT: C 154 ASP cc_start: 0.7530 (m-30) cc_final: 0.7283 (m-30) REVERT: C 175 GLN cc_start: 0.7974 (pt0) cc_final: 0.7555 (pp30) REVERT: C 215 GLU cc_start: 0.7278 (tp30) cc_final: 0.6693 (tp30) REVERT: E 19 LYS cc_start: 0.8430 (tttp) cc_final: 0.8096 (tppp) REVERT: E 38 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7772 (ptp-170) outliers start: 6 outliers final: 2 residues processed: 187 average time/residue: 1.1097 time to fit residues: 221.4255 Evaluate side-chains 154 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 188 HIS B 346 ASN B 347 ASN C 62 HIS C 239 ASN E 39 GLN E 113 GLN E 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.204039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147621 restraints weight = 9855.319| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.51 r_work: 0.3498 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8567 Z= 0.276 Angle : 0.684 12.382 11660 Z= 0.358 Chirality : 0.045 0.236 1376 Planarity : 0.005 0.057 1489 Dihedral : 6.330 37.657 1219 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.53 % Allowed : 16.59 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.22), residues: 1120 helix: -3.37 (0.19), residues: 365 sheet: -1.75 (0.29), residues: 280 loop : -2.04 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 PHE 0.019 0.002 PHE C 151 TYR 0.019 0.002 TYR C 59 ARG 0.006 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.876 Fit side-chains REVERT: A 93 MET cc_start: 0.6872 (mmm) cc_final: 0.6633 (tpt) REVERT: A 122 ASP cc_start: 0.6693 (m-30) cc_final: 0.6225 (t0) REVERT: A 196 ASN cc_start: 0.7359 (m110) cc_final: 0.7015 (m110) REVERT: A 209 ILE cc_start: 0.7511 (pt) cc_final: 0.7297 (mp) REVERT: A 302 TYR cc_start: 0.8009 (m-80) cc_final: 0.7745 (m-80) REVERT: B 24 ARG cc_start: 0.7648 (ttp-110) cc_final: 0.6997 (ttp-110) REVERT: B 262 THR cc_start: 0.8569 (p) cc_final: 0.8289 (t) REVERT: C 154 ASP cc_start: 0.7793 (m-30) cc_final: 0.7482 (m-30) REVERT: C 175 GLN cc_start: 0.8310 (pt0) cc_final: 0.7609 (pp30) REVERT: E 19 LYS cc_start: 0.8494 (tttp) cc_final: 0.8023 (tppp) REVERT: E 234 GLU cc_start: 0.8225 (pt0) cc_final: 0.7774 (pt0) outliers start: 30 outliers final: 12 residues processed: 195 average time/residue: 1.0650 time to fit residues: 222.4609 Evaluate side-chains 167 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.206302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150115 restraints weight = 9948.503| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.15 r_work: 0.3557 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8567 Z= 0.196 Angle : 0.612 12.580 11660 Z= 0.318 Chirality : 0.044 0.163 1376 Planarity : 0.004 0.054 1489 Dihedral : 5.776 40.551 1219 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.94 % Allowed : 18.94 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.23), residues: 1120 helix: -2.51 (0.23), residues: 363 sheet: -1.42 (0.28), residues: 283 loop : -1.83 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.018 0.001 PHE C 241 TYR 0.016 0.002 TYR A 180 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6415 (m-30) cc_final: 0.5967 (t0) REVERT: A 180 TYR cc_start: 0.7317 (m-80) cc_final: 0.6754 (m-10) REVERT: A 196 ASN cc_start: 0.7376 (m110) cc_final: 0.7153 (m110) REVERT: A 302 TYR cc_start: 0.8184 (m-80) cc_final: 0.7908 (m-80) REVERT: B 9 ASP cc_start: 0.8298 (m-30) cc_final: 0.7871 (m-30) REVERT: B 24 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7276 (ttp-110) REVERT: B 262 THR cc_start: 0.8545 (p) cc_final: 0.8239 (t) REVERT: B 274 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.5457 (p90) REVERT: C 175 GLN cc_start: 0.8404 (pt0) cc_final: 0.7725 (pp30) REVERT: C 275 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.8014 (m) REVERT: C 325 MET cc_start: 0.7995 (tpp) cc_final: 0.7640 (mmt) REVERT: E 13 GLN cc_start: 0.7328 (pp30) cc_final: 0.7022 (pp30) REVERT: E 19 LYS cc_start: 0.8473 (tttp) cc_final: 0.7934 (tppp) REVERT: E 76 LYS cc_start: 0.8061 (mptt) cc_final: 0.7841 (mttp) REVERT: E 234 GLU cc_start: 0.8398 (pt0) cc_final: 0.8072 (pt0) outliers start: 42 outliers final: 19 residues processed: 191 average time/residue: 1.0641 time to fit residues: 217.5588 Evaluate side-chains 168 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151134 restraints weight = 9947.228| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.15 r_work: 0.3573 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8567 Z= 0.174 Angle : 0.593 12.294 11660 Z= 0.304 Chirality : 0.043 0.179 1376 Planarity : 0.004 0.052 1489 Dihedral : 5.358 43.585 1219 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.71 % Allowed : 20.47 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1120 helix: -1.98 (0.25), residues: 364 sheet: -1.34 (0.28), residues: 293 loop : -1.66 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.011 0.001 PHE B 334 TYR 0.012 0.001 TYR E 103 ARG 0.009 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6177 (m-30) cc_final: 0.5812 (t70) REVERT: A 180 TYR cc_start: 0.7293 (m-80) cc_final: 0.6646 (m-10) REVERT: A 302 TYR cc_start: 0.8048 (m-80) cc_final: 0.7844 (m-80) REVERT: B 9 ASP cc_start: 0.8355 (m-30) cc_final: 0.7903 (m-30) REVERT: B 21 ARG cc_start: 0.8215 (ptp90) cc_final: 0.7756 (mtm110) REVERT: B 24 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7308 (ttp-110) REVERT: B 262 THR cc_start: 0.8464 (p) cc_final: 0.8263 (t) REVERT: C 175 GLN cc_start: 0.8203 (pt0) cc_final: 0.7584 (pp30) REVERT: C 234 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: C 275 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (m) REVERT: C 325 MET cc_start: 0.7997 (tpp) cc_final: 0.7642 (mmt) REVERT: E 19 LYS cc_start: 0.8449 (tttp) cc_final: 0.7896 (tppp) REVERT: E 189 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7793 (mp) REVERT: E 234 GLU cc_start: 0.8411 (pt0) cc_final: 0.8138 (pt0) outliers start: 40 outliers final: 18 residues processed: 191 average time/residue: 0.9948 time to fit residues: 204.1154 Evaluate side-chains 170 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.206518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.149701 restraints weight = 9906.875| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.19 r_work: 0.3562 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8567 Z= 0.199 Angle : 0.592 12.225 11660 Z= 0.306 Chirality : 0.043 0.188 1376 Planarity : 0.004 0.051 1489 Dihedral : 5.285 47.398 1219 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.82 % Allowed : 22.00 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.24), residues: 1120 helix: -1.61 (0.26), residues: 367 sheet: -1.16 (0.30), residues: 264 loop : -1.60 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.029 0.002 PHE B 189 TYR 0.013 0.001 TYR E 103 ARG 0.008 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6178 (m-30) cc_final: 0.5706 (t0) REVERT: A 180 TYR cc_start: 0.7243 (m-80) cc_final: 0.6517 (m-10) REVERT: B 21 ARG cc_start: 0.8226 (ptp90) cc_final: 0.7792 (mtm110) REVERT: B 24 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7330 (ttp-110) REVERT: B 308 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: C 175 GLN cc_start: 0.8241 (pt0) cc_final: 0.7633 (pp30) REVERT: C 275 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7916 (m) REVERT: C 325 MET cc_start: 0.8068 (tpp) cc_final: 0.7713 (mmt) REVERT: D 47 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: E 19 LYS cc_start: 0.8447 (tttp) cc_final: 0.7941 (tppp) REVERT: E 186 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 189 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7817 (mp) outliers start: 41 outliers final: 23 residues processed: 174 average time/residue: 1.1029 time to fit residues: 205.2054 Evaluate side-chains 169 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.208536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.153121 restraints weight = 9892.869| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.53 r_work: 0.3577 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8567 Z= 0.162 Angle : 0.568 12.038 11660 Z= 0.294 Chirality : 0.043 0.178 1376 Planarity : 0.004 0.049 1489 Dihedral : 5.110 50.974 1219 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.59 % Allowed : 22.47 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.25), residues: 1120 helix: -1.23 (0.26), residues: 368 sheet: -0.89 (0.30), residues: 268 loop : -1.54 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.026 0.001 PHE B 189 TYR 0.011 0.001 TYR E 173 ARG 0.009 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7939 (mm) cc_final: 0.7433 (tp) REVERT: A 122 ASP cc_start: 0.6129 (m-30) cc_final: 0.5726 (t70) REVERT: A 180 TYR cc_start: 0.7141 (m-80) cc_final: 0.6526 (m-10) REVERT: A 218 LEU cc_start: 0.7172 (mm) cc_final: 0.6893 (tp) REVERT: B 9 ASP cc_start: 0.8209 (m-30) cc_final: 0.7696 (m-30) REVERT: B 21 ARG cc_start: 0.7960 (ptp90) cc_final: 0.7608 (mtm110) REVERT: B 24 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7231 (ttp-110) REVERT: B 308 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: C 175 GLN cc_start: 0.8095 (pt0) cc_final: 0.7584 (pp30) REVERT: C 252 LEU cc_start: 0.8660 (tt) cc_final: 0.8297 (tt) REVERT: C 275 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7726 (m) REVERT: C 325 MET cc_start: 0.7867 (tpp) cc_final: 0.7496 (mmt) REVERT: E 19 LYS cc_start: 0.8401 (tttp) cc_final: 0.7926 (tppp) REVERT: E 186 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7555 (tm-30) REVERT: E 189 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7798 (mp) outliers start: 39 outliers final: 24 residues processed: 188 average time/residue: 1.2428 time to fit residues: 249.3213 Evaluate side-chains 174 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 308 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151342 restraints weight = 9961.036| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.22 r_work: 0.3592 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8567 Z= 0.182 Angle : 0.589 11.960 11660 Z= 0.305 Chirality : 0.043 0.185 1376 Planarity : 0.004 0.049 1489 Dihedral : 5.102 54.025 1219 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.71 % Allowed : 23.76 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1120 helix: -0.96 (0.27), residues: 362 sheet: -0.77 (0.31), residues: 266 loop : -1.38 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS A 146 PHE 0.025 0.002 PHE C 241 TYR 0.025 0.002 TYR A 205 ARG 0.011 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7729 (mm) cc_final: 0.7527 (tp) REVERT: A 122 ASP cc_start: 0.6131 (m-30) cc_final: 0.5623 (t0) REVERT: A 180 TYR cc_start: 0.7142 (m-80) cc_final: 0.6452 (m-10) REVERT: A 218 LEU cc_start: 0.7207 (mm) cc_final: 0.6915 (tp) REVERT: A 248 LYS cc_start: 0.5482 (tppp) cc_final: 0.5130 (mppt) REVERT: B 21 ARG cc_start: 0.8176 (ptp90) cc_final: 0.7842 (mtm110) REVERT: B 24 ARG cc_start: 0.7840 (ttp-110) cc_final: 0.7283 (ttp-110) REVERT: B 308 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: C 175 GLN cc_start: 0.8185 (pt0) cc_final: 0.7603 (pp30) REVERT: C 252 LEU cc_start: 0.8641 (tt) cc_final: 0.8226 (tt) REVERT: C 275 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7903 (m) REVERT: C 325 MET cc_start: 0.8066 (tpp) cc_final: 0.7714 (mmt) REVERT: E 19 LYS cc_start: 0.8291 (tttp) cc_final: 0.7851 (tppp) REVERT: E 186 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7668 (tm-30) REVERT: E 189 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7882 (mp) outliers start: 40 outliers final: 25 residues processed: 179 average time/residue: 1.1378 time to fit residues: 217.7667 Evaluate side-chains 176 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 38 optimal weight: 0.0000 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.211950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159154 restraints weight = 9968.604| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.46 r_work: 0.3641 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8567 Z= 0.140 Angle : 0.560 11.894 11660 Z= 0.290 Chirality : 0.042 0.171 1376 Planarity : 0.004 0.047 1489 Dihedral : 4.918 59.989 1219 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.65 % Allowed : 25.06 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.26), residues: 1120 helix: -0.64 (0.28), residues: 361 sheet: -0.75 (0.31), residues: 267 loop : -1.27 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.028 0.001 PHE C 241 TYR 0.010 0.001 TYR E 173 ARG 0.011 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.5991 (m-30) cc_final: 0.5611 (t0) REVERT: A 218 LEU cc_start: 0.7171 (mm) cc_final: 0.6918 (tp) REVERT: A 248 LYS cc_start: 0.5378 (tppp) cc_final: 0.5009 (mppt) REVERT: B 21 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7617 (mtt90) REVERT: B 24 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7146 (ttp-110) REVERT: B 308 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: C 175 GLN cc_start: 0.7960 (pt0) cc_final: 0.7546 (pp30) REVERT: C 252 LEU cc_start: 0.8625 (tt) cc_final: 0.8326 (tt) REVERT: C 275 SER cc_start: 0.8024 (OUTLIER) cc_final: 0.7661 (m) REVERT: C 325 MET cc_start: 0.7780 (tpp) cc_final: 0.7422 (mmt) REVERT: E 18 ARG cc_start: 0.7154 (ttt90) cc_final: 0.6932 (ttt90) REVERT: E 19 LYS cc_start: 0.8252 (tttp) cc_final: 0.7876 (tppp) REVERT: E 160 ARG cc_start: 0.6372 (mmm160) cc_final: 0.6168 (mmm160) REVERT: E 186 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7447 (tm-30) REVERT: E 214 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.4996 (tp) REVERT: E 220 GLU cc_start: 0.7366 (mp0) cc_final: 0.6833 (mp0) outliers start: 31 outliers final: 18 residues processed: 174 average time/residue: 1.0829 time to fit residues: 201.9570 Evaluate side-chains 169 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 15 optimal weight: 50.0000 chunk 54 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 61 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.210259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156065 restraints weight = 10052.073| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.54 r_work: 0.3608 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8567 Z= 0.171 Angle : 0.578 11.385 11660 Z= 0.300 Chirality : 0.043 0.161 1376 Planarity : 0.004 0.045 1489 Dihedral : 4.928 56.498 1219 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.82 % Allowed : 26.71 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1120 helix: -0.54 (0.28), residues: 361 sheet: -0.70 (0.31), residues: 265 loop : -1.35 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.026 0.001 PHE C 241 TYR 0.024 0.001 TYR A 205 ARG 0.008 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6050 (m-30) cc_final: 0.5676 (t0) REVERT: A 205 TYR cc_start: 0.5993 (t80) cc_final: 0.5786 (t80) REVERT: A 248 LYS cc_start: 0.5518 (tppp) cc_final: 0.5143 (mppt) REVERT: A 273 TYR cc_start: 0.6687 (m-80) cc_final: 0.6472 (m-80) REVERT: B 24 ARG cc_start: 0.7688 (ttp-110) cc_final: 0.7148 (ttp-110) REVERT: B 308 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: C 175 GLN cc_start: 0.7931 (pt0) cc_final: 0.7570 (pp30) REVERT: C 275 SER cc_start: 0.7970 (OUTLIER) cc_final: 0.7633 (m) REVERT: C 325 MET cc_start: 0.7828 (tpp) cc_final: 0.7442 (mmt) REVERT: E 19 LYS cc_start: 0.8279 (tttp) cc_final: 0.7909 (tppp) REVERT: E 186 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7488 (tm-30) REVERT: E 214 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.4964 (tp) REVERT: E 220 GLU cc_start: 0.7380 (mp0) cc_final: 0.6868 (mp0) outliers start: 24 outliers final: 17 residues processed: 168 average time/residue: 1.0456 time to fit residues: 188.3591 Evaluate side-chains 167 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 273 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 0.0030 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.0030 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.211717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.156993 restraints weight = 9948.704| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.16 r_work: 0.3656 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8567 Z= 0.151 Angle : 0.575 11.051 11660 Z= 0.299 Chirality : 0.043 0.161 1376 Planarity : 0.004 0.045 1489 Dihedral : 4.825 50.286 1219 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.35 % Allowed : 27.29 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.26), residues: 1120 helix: -0.39 (0.29), residues: 361 sheet: -0.66 (0.31), residues: 267 loop : -1.31 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 47 HIS 0.002 0.001 HIS C 91 PHE 0.025 0.001 PHE C 241 TYR 0.024 0.001 TYR A 205 ARG 0.008 0.000 ARG C 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6189 (m-30) cc_final: 0.5803 (t0) REVERT: A 205 TYR cc_start: 0.6019 (t80) cc_final: 0.5784 (t80) REVERT: A 300 LEU cc_start: 0.8188 (tp) cc_final: 0.7909 (tt) REVERT: B 21 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7732 (mtm110) REVERT: B 24 ARG cc_start: 0.7793 (ttp-110) cc_final: 0.7220 (ttp-110) REVERT: B 308 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: C 175 GLN cc_start: 0.7963 (pt0) cc_final: 0.7521 (pp30) REVERT: C 275 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7830 (m) REVERT: C 325 MET cc_start: 0.8007 (tpp) cc_final: 0.7623 (mmt) REVERT: D 47 GLU cc_start: 0.6933 (mp0) cc_final: 0.6592 (mp0) REVERT: E 186 GLN cc_start: 0.7792 (tm-30) cc_final: 0.7565 (tm-30) REVERT: E 214 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.4974 (tp) REVERT: E 220 GLU cc_start: 0.7352 (mp0) cc_final: 0.6836 (mp0) outliers start: 20 outliers final: 15 residues processed: 164 average time/residue: 1.1904 time to fit residues: 208.7559 Evaluate side-chains 163 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.3980 chunk 41 optimal weight: 0.0570 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 30.0000 chunk 108 optimal weight: 10.0000 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 GLN C 88 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.211280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156580 restraints weight = 10062.307| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.18 r_work: 0.3641 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8567 Z= 0.163 Angle : 0.591 10.882 11660 Z= 0.303 Chirality : 0.043 0.156 1376 Planarity : 0.004 0.045 1489 Dihedral : 4.772 43.606 1219 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.82 % Allowed : 27.06 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1120 helix: -0.31 (0.29), residues: 361 sheet: -0.61 (0.32), residues: 265 loop : -1.33 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 47 HIS 0.003 0.001 HIS C 91 PHE 0.024 0.001 PHE C 241 TYR 0.023 0.001 TYR A 205 ARG 0.008 0.000 ARG C 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7987.59 seconds wall clock time: 139 minutes 23.12 seconds (8363.12 seconds total)