Starting phenix.real_space_refine on Thu Jul 2 10:51:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xav_33100/07_2026/7xav_33100.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xav_33100/07_2026/7xav_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_33100/07_2026/7xav_33100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2026/7xav_33100.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2026/7xav_33100.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2026/7xav_33100.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2026/7xav_33100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2026/7xav_33100.cif" } resolution = 2.87 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= 0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'PHE:plan': 11, 'TYR:plan': 1, 'ARG:plan': 6, 'ASP:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TRP:plan': 5, 'ASN:plan1': 3, 'GLN:plan1': 2} 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: {'GLU:plan': 9, 'ASP:plan': 6, 'HIS:plan': 1, 'ARG:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} 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} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'DTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.75, per 1000 atoms: 0.21 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: 0.71 Conformation dependent library (CDL) restraints added in 450.9 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: 0.24 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: 0.92 Time building geometry restraints manager: 0.89 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 - 16.81: 4523 16.81 - 33.62: 441 33.62 - 50.42: 84 50.42 - 67.23: 14 67.23 - 84.04: 7 Dihedral angle restraints: 5069 sinusoidal: 1768 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 5066 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.180 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 8573 Z= 0.399 Angle : 1.053 17.673 11673 Z= 0.568 Chirality : 0.064 0.270 1376 Planarity : 0.007 0.079 1489 Dihedral : 14.229 84.039 2919 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 7.78 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 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: -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 ARG 0.006 0.001 ARG B 21 TYR 0.035 0.003 TYR C 105 PHE 0.042 0.004 PHE C 151 TRP 0.023 0.003 TRP C 99 HIS 0.008 0.002 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00916 / 0.40 ( 8567) covalent geometry : angle 1.05122 / 0.57 (11660) SS BOND : bond 0.01405 / 0.75 ( 5) SS BOND : angle 2.55916 / 1.40 ( 10) hydrogen bonds : bond 0.29973 / 20.07 ( 289) hydrogen bonds : angle 11.03237 / 7.65 ( 795) link_TRANS : bond 0.00501 / 0.26 ( 1) link_TRANS : angle 0.28799 / 0.15 ( 3) *********************** 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 : 0.245 Fit side-chains REVERT: A 122 ASP cc_start: 0.6663 (m-30) cc_final: 0.6404 (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: 0.7469 (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: 0.7446 (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: 0.6770 (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: 0.7785 (ptp-170) outliers start: 6 outliers final: 2 residues processed: 187 average time/residue: 0.4477 time to fit residues: 89.4812 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 : 0.202 ------------------------------------------------------------------------------- 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 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4315 r_free = 0.4315 target = 0.204538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147712 restraints weight = 9996.149| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.16 r_work: 0.3522 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8573 Z= 0.173 Angle : 0.677 12.300 11673 Z= 0.354 Chirality : 0.045 0.234 1376 Planarity : 0.005 0.057 1489 Dihedral : 6.512 60.424 1218 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.53 % Allowed : 16.47 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.22), residues: 1120 helix: -3.37 (0.19), residues: 364 sheet: -1.73 (0.29), residues: 280 loop : -2.00 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 160 TYR 0.018 0.002 TYR C 59 PHE 0.017 0.002 PHE C 151 TRP 0.015 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8567) covalent geometry : angle 0.67525 / 0.35 (11660) SS BOND : bond 0.00835 / 0.44 ( 5) SS BOND : angle 1.62470 / 1.07 ( 10) hydrogen bonds : bond 0.04543 / 3.21 ( 289) hydrogen bonds : angle 6.30511 / 4.39 ( 795) link_TRANS : bond 0.00421 / 0.22 ( 1) link_TRANS : angle 0.36344 / 0.19 ( 3) *********************** 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 208 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.331 Fit side-chains REVERT: A 93 MET cc_start: 0.6960 (mmm) cc_final: 0.6705 (tpt) REVERT: A 122 ASP cc_start: 0.6937 (m-30) cc_final: 0.6366 (t0) REVERT: A 196 ASN cc_start: 0.7319 (m110) cc_final: 0.6984 (m110) REVERT: A 209 ILE cc_start: 0.7546 (pt) cc_final: 0.7341 (mp) REVERT: A 302 TYR cc_start: 0.8152 (m-80) cc_final: 0.7841 (m-80) REVERT: B 24 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7138 (ttp-110) REVERT: B 262 THR cc_start: 0.8567 (p) cc_final: 0.8266 (t) REVERT: B 333 GLN cc_start: 0.7919 (tp40) cc_final: 0.7336 (tp40) REVERT: C 154 ASP cc_start: 0.7957 (m-30) cc_final: 0.7668 (m-30) REVERT: C 175 GLN cc_start: 0.8416 (pt0) cc_final: 0.7723 (pp30) REVERT: C 197 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7583 (mmm-85) REVERT: E 19 LYS cc_start: 0.8481 (tttp) cc_final: 0.8005 (tppp) REVERT: E 234 GLU cc_start: 0.8465 (pt0) cc_final: 0.8083 (pt0) outliers start: 30 outliers final: 12 residues processed: 195 average time/residue: 0.4407 time to fit residues: 92.3856 Evaluate side-chains 169 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 19 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 102 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.205190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.148591 restraints weight = 9813.324| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.16 r_work: 0.3536 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8573 Z= 0.155 Angle : 0.630 12.487 11673 Z= 0.328 Chirality : 0.044 0.163 1376 Planarity : 0.005 0.056 1489 Dihedral : 6.017 52.156 1218 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.82 % Allowed : 18.94 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.23), residues: 1120 helix: -2.51 (0.23), residues: 362 sheet: -1.45 (0.29), residues: 276 loop : -1.82 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 160 TYR 0.016 0.002 TYR E 103 PHE 0.018 0.002 PHE C 241 TRP 0.013 0.001 TRP C 99 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8567) covalent geometry : angle 0.62791 / 0.33 (11660) SS BOND : bond 0.01118 / 0.55 ( 5) SS BOND : angle 1.94866 / 1.09 ( 10) hydrogen bonds : bond 0.03711 / 2.62 ( 289) hydrogen bonds : angle 5.61309 / 3.91 ( 795) link_TRANS : bond 0.00171 / 0.09 ( 1) link_TRANS : angle 0.16391 / 0.09 ( 3) *********************** 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 201 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.254 Fit side-chains REVERT: A 122 ASP cc_start: 0.6310 (m-30) cc_final: 0.6010 (t0) REVERT: A 180 TYR cc_start: 0.7333 (m-80) cc_final: 0.6732 (m-10) REVERT: A 196 ASN cc_start: 0.7333 (m110) cc_final: 0.7112 (m110) REVERT: A 302 TYR cc_start: 0.8149 (m-80) cc_final: 0.7911 (m-80) REVERT: B 9 ASP cc_start: 0.8341 (m-30) cc_final: 0.7883 (m-30) REVERT: B 24 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7309 (ttp-110) REVERT: B 262 THR cc_start: 0.8618 (p) cc_final: 0.8316 (t) REVERT: B 333 GLN cc_start: 0.7861 (tp40) cc_final: 0.7368 (tp40) REVERT: C 154 ASP cc_start: 0.7948 (m-30) cc_final: 0.7613 (m-30) REVERT: C 175 GLN cc_start: 0.8404 (pt0) cc_final: 0.7715 (pp30) REVERT: C 275 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.8058 (m) REVERT: C 284 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7047 (tp) REVERT: C 325 MET cc_start: 0.8004 (tpp) cc_final: 0.7582 (mmt) REVERT: D 62 ARG cc_start: 0.5733 (mtt90) cc_final: 0.5476 (mtt90) REVERT: E 19 LYS cc_start: 0.8479 (tttp) cc_final: 0.7918 (tppp) REVERT: E 76 LYS cc_start: 0.8061 (mptt) cc_final: 0.7838 (mttp) REVERT: E 234 GLU cc_start: 0.8479 (pt0) cc_final: 0.8147 (pt0) outliers start: 41 outliers final: 18 residues processed: 187 average time/residue: 0.4256 time to fit residues: 85.4054 Evaluate side-chains 165 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 279 SER Chi-restraints excluded: chain A residue 310 ILE 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 219 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 LEU 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 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 110 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 50.0000 chunk 71 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 GLN C 239 ASN C 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.203590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145941 restraints weight = 10076.992| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.59 r_work: 0.3496 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8573 Z= 0.184 Angle : 0.651 12.132 11673 Z= 0.337 Chirality : 0.045 0.193 1376 Planarity : 0.004 0.056 1489 Dihedral : 5.919 50.189 1218 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.65 % Allowed : 20.24 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.78 (0.24), residues: 1120 helix: -2.07 (0.25), residues: 362 sheet: -1.45 (0.28), residues: 284 loop : -1.71 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.017 0.002 TYR E 103 PHE 0.021 0.002 PHE C 151 TRP 0.015 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 8567) covalent geometry : angle 0.64773 / 0.34 (11660) SS BOND : bond 0.01224 / 0.62 ( 5) SS BOND : angle 2.33308 / 1.34 ( 10) hydrogen bonds : bond 0.03629 / 2.57 ( 289) hydrogen bonds : angle 5.41980 / 3.76 ( 795) link_TRANS : bond 0.00173 / 0.09 ( 1) link_TRANS : angle 0.35862 / 0.19 ( 3) *********************** 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 195 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.335 Fit side-chains REVERT: A 122 ASP cc_start: 0.5942 (m-30) cc_final: 0.5693 (t0) REVERT: A 180 TYR cc_start: 0.7347 (m-80) cc_final: 0.6716 (m-10) REVERT: A 196 ASN cc_start: 0.7474 (m110) cc_final: 0.7267 (m110) REVERT: A 302 TYR cc_start: 0.7899 (m-80) cc_final: 0.7689 (m-80) REVERT: B 9 ASP cc_start: 0.8266 (m-30) cc_final: 0.7741 (m-30) REVERT: B 24 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7057 (ttp-110) REVERT: B 191 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.5447 (p90) REVERT: B 262 THR cc_start: 0.8649 (p) cc_final: 0.8344 (t) REVERT: C 175 GLN cc_start: 0.8315 (pt0) cc_final: 0.7577 (pp30) REVERT: C 217 MET cc_start: 0.6741 (ppp) cc_final: 0.6534 (pp-130) REVERT: C 275 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7975 (m) REVERT: C 325 MET cc_start: 0.7824 (tpp) cc_final: 0.7379 (mmt) REVERT: E 19 LYS cc_start: 0.8456 (tttp) cc_final: 0.7873 (tppp) REVERT: E 76 LYS cc_start: 0.8128 (mptt) cc_final: 0.7921 (mttp) REVERT: E 83 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7007 (ptt) REVERT: E 234 GLU cc_start: 0.8312 (pt0) cc_final: 0.7944 (pt0) outliers start: 48 outliers final: 32 residues processed: 179 average time/residue: 0.4690 time to fit residues: 90.1456 Evaluate side-chains 176 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL 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 37 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 191 PHE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL 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 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 276 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 290 ASP 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 83 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 0.0970 chunk 76 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 46 optimal weight: 0.0370 chunk 27 optimal weight: 8.9990 overall best weight: 1.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 ASN C 259 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.205262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147449 restraints weight = 10024.104| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.44 r_work: 0.3511 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8573 Z= 0.147 Angle : 0.612 12.325 11673 Z= 0.316 Chirality : 0.044 0.148 1376 Planarity : 0.004 0.054 1489 Dihedral : 5.650 53.181 1218 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.94 % Allowed : 21.41 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.24), residues: 1120 helix: -1.75 (0.25), residues: 366 sheet: -1.43 (0.29), residues: 286 loop : -1.64 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.013 0.001 TYR E 103 PHE 0.028 0.002 PHE B 189 TRP 0.013 0.001 TRP C 99 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8567) covalent geometry : angle 0.61022 / 0.32 (11660) SS BOND : bond 0.01002 / 0.50 ( 5) SS BOND : angle 1.77511 / 0.99 ( 10) hydrogen bonds : bond 0.03271 / 2.30 ( 289) hydrogen bonds : angle 5.13367 / 3.55 ( 795) link_TRANS : bond 0.00065 / 0.03 ( 1) link_TRANS : angle 0.38093 / 0.22 ( 3) *********************** 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 200 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.329 Fit side-chains REVERT: A 122 ASP cc_start: 0.5917 (m-30) cc_final: 0.5591 (t0) REVERT: A 180 TYR cc_start: 0.7290 (m-80) cc_final: 0.6578 (m-10) REVERT: B 9 ASP cc_start: 0.8256 (m-30) cc_final: 0.7761 (m-30) REVERT: B 21 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7587 (mtm110) REVERT: B 24 ARG cc_start: 0.7810 (ttp-110) cc_final: 0.7253 (ttp-110) REVERT: B 262 THR cc_start: 0.8602 (p) cc_final: 0.8312 (t) REVERT: C 175 GLN cc_start: 0.8186 (pt0) cc_final: 0.7579 (pp30) REVERT: C 275 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7903 (m) REVERT: C 290 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.6181 (p0) REVERT: C 325 MET cc_start: 0.7798 (tpp) cc_final: 0.7364 (mmt) REVERT: D 47 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6546 (pm20) REVERT: E 19 LYS cc_start: 0.8475 (tttp) cc_final: 0.7952 (tppp) outliers start: 42 outliers final: 25 residues processed: 185 average time/residue: 0.4866 time to fit residues: 96.6081 Evaluate side-chains 174 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 37 LEU 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 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 213 VAL Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 273 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 46 optimal weight: 0.0570 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 237 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 = 0.4334 r_free = 0.4334 target = 0.206800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150030 restraints weight = 9947.112| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.19 r_work: 0.3566 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8573 Z= 0.120 Angle : 0.596 12.386 11673 Z= 0.305 Chirality : 0.043 0.212 1376 Planarity : 0.004 0.052 1489 Dihedral : 5.433 56.108 1218 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.06 % Allowed : 22.59 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.24 (0.25), residues: 1120 helix: -1.42 (0.26), residues: 368 sheet: -1.19 (0.30), residues: 267 loop : -1.54 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 304 TYR 0.016 0.001 TYR E 173 PHE 0.025 0.002 PHE C 241 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8567) covalent geometry : angle 0.59529 / 0.30 (11660) SS BOND : bond 0.00803 / 0.40 ( 5) SS BOND : angle 1.43662 / 0.78 ( 10) hydrogen bonds : bond 0.02967 / 2.06 ( 289) hydrogen bonds : angle 4.91291 / 3.40 ( 795) link_TRANS : bond 0.00003 / 0.00 ( 1) link_TRANS : angle 0.40008 / 0.23 ( 3) *********************** 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 205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.291 Fit side-chains REVERT: A 122 ASP cc_start: 0.6260 (m-30) cc_final: 0.5811 (t70) REVERT: A 180 TYR cc_start: 0.7229 (m-80) cc_final: 0.6581 (m-10) REVERT: A 218 LEU cc_start: 0.7360 (mm) cc_final: 0.7023 (tp) REVERT: B 21 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7793 (mtm110) REVERT: B 24 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7318 (ttp-110) REVERT: B 262 THR cc_start: 0.8504 (p) cc_final: 0.8250 (t) REVERT: B 274 PHE cc_start: 0.5919 (OUTLIER) cc_final: 0.5433 (p90) REVERT: B 308 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: C 175 GLN cc_start: 0.8170 (pt0) cc_final: 0.7562 (pp30) REVERT: C 252 LEU cc_start: 0.8669 (tt) cc_final: 0.8263 (tt) REVERT: C 275 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.8110 (m) REVERT: C 325 MET cc_start: 0.8009 (tpp) cc_final: 0.7613 (mmt) REVERT: D 47 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6527 (pm20) REVERT: E 18 ARG cc_start: 0.7523 (tpt90) cc_final: 0.7273 (mtt-85) REVERT: E 19 LYS cc_start: 0.8431 (tttp) cc_final: 0.7895 (tppp) REVERT: E 160 ARG cc_start: 0.6427 (mmm160) cc_final: 0.6212 (mmm160) REVERT: E 186 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 214 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.4899 (tp) outliers start: 43 outliers final: 21 residues processed: 189 average time/residue: 0.4263 time to fit residues: 86.5894 Evaluate side-chains 178 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 218 VAL 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 219 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 276 VAL 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 214 LEU Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.204226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146557 restraints weight = 10009.641| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.55 r_work: 0.3486 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8573 Z= 0.189 Angle : 0.651 11.931 11673 Z= 0.335 Chirality : 0.046 0.186 1376 Planarity : 0.004 0.054 1489 Dihedral : 5.656 55.266 1218 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.00 % Allowed : 22.71 % 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 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: -2.03 (0.25), residues: 1120 helix: -1.16 (0.27), residues: 353 sheet: -1.32 (0.29), residues: 286 loop : -1.31 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 304 TYR 0.015 0.002 TYR E 103 PHE 0.028 0.002 PHE C 241 TRP 0.016 0.002 TRP C 99 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 8567) covalent geometry : angle 0.64877 / 0.33 (11660) SS BOND : bond 0.01190 / 0.62 ( 5) SS BOND : angle 2.13709 / 1.25 ( 10) hydrogen bonds : bond 0.03343 / 2.35 ( 289) hydrogen bonds : angle 5.11211 / 3.54 ( 795) link_TRANS : bond 0.00072 / 0.04 ( 1) link_TRANS : angle 0.33488 / 0.19 ( 3) *********************** 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 204 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.322 Fit side-chains REVERT: A 46 LEU cc_start: 0.7931 (mm) cc_final: 0.7712 (tp) REVERT: A 122 ASP cc_start: 0.5963 (m-30) cc_final: 0.5586 (t0) REVERT: A 180 TYR cc_start: 0.7179 (m-80) cc_final: 0.6552 (m-10) REVERT: B 21 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7570 (mtm110) REVERT: B 24 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7152 (ttp-110) REVERT: B 262 THR cc_start: 0.8681 (p) cc_final: 0.8376 (t) REVERT: B 308 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: C 154 ASP cc_start: 0.7796 (m-30) cc_final: 0.7468 (m-30) REVERT: C 175 GLN cc_start: 0.8232 (pt0) cc_final: 0.7557 (pp30) REVERT: C 275 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.7983 (m) REVERT: C 325 MET cc_start: 0.7837 (tpp) cc_final: 0.7413 (mmt) REVERT: E 19 LYS cc_start: 0.8460 (tttp) cc_final: 0.8064 (tppp) REVERT: E 43 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7379 (tppp) REVERT: E 67 ARG cc_start: 0.7223 (mtm110) cc_final: 0.7022 (ttp80) REVERT: E 186 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7511 (tm-30) REVERT: E 214 LEU cc_start: 0.5476 (OUTLIER) cc_final: 0.4626 (tp) REVERT: E 220 GLU cc_start: 0.7520 (mp0) cc_final: 0.6932 (mp0) outliers start: 51 outliers final: 28 residues processed: 187 average time/residue: 0.4785 time to fit residues: 95.9087 Evaluate side-chains 183 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 311 LEU 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 201 VAL Chi-restraints excluded: chain B residue 218 VAL 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 213 VAL 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 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 214 LEU 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 41 optimal weight: 5.9990 chunk 14 optimal weight: 40.0000 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.203986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146018 restraints weight = 9924.267| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.20 r_work: 0.3510 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8573 Z= 0.179 Angle : 0.648 11.972 11673 Z= 0.333 Chirality : 0.046 0.177 1376 Planarity : 0.004 0.054 1489 Dihedral : 5.662 55.870 1218 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.71 % Allowed : 24.47 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.96 (0.25), residues: 1120 helix: -1.01 (0.27), residues: 353 sheet: -1.36 (0.29), residues: 288 loop : -1.30 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 304 TYR 0.015 0.002 TYR E 103 PHE 0.030 0.002 PHE C 241 TRP 0.016 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 8567) covalent geometry : angle 0.64614 / 0.33 (11660) SS BOND : bond 0.01145 / 0.57 ( 5) SS BOND : angle 1.98623 / 1.13 ( 10) hydrogen bonds : bond 0.03289 / 2.30 ( 289) hydrogen bonds : angle 5.12453 / 3.54 ( 795) link_TRANS : bond 0.00002 / 0.00 ( 1) link_TRANS : angle 0.60155 / 0.33 ( 3) *********************** 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 195 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.285 Fit side-chains REVERT: A 180 TYR cc_start: 0.7302 (m-80) cc_final: 0.6615 (m-10) REVERT: B 21 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7824 (mtm110) REVERT: B 24 ARG cc_start: 0.7898 (ttp-110) cc_final: 0.7357 (ttp-110) REVERT: B 262 THR cc_start: 0.8674 (p) cc_final: 0.8320 (t) REVERT: B 308 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: C 154 ASP cc_start: 0.7994 (m-30) cc_final: 0.7688 (m-30) REVERT: C 175 GLN cc_start: 0.8340 (pt0) cc_final: 0.7646 (pp30) REVERT: C 275 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.8104 (m) REVERT: C 325 MET cc_start: 0.8011 (tpp) cc_final: 0.7707 (mmt) REVERT: E 18 ARG cc_start: 0.7610 (tpt90) cc_final: 0.7227 (mtt-85) REVERT: E 19 LYS cc_start: 0.8448 (tttp) cc_final: 0.7923 (tppp) REVERT: E 43 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7309 (tppp) REVERT: E 82 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6953 (tp40) REVERT: E 89 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6912 (tm-30) REVERT: E 186 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 214 LEU cc_start: 0.5643 (OUTLIER) cc_final: 0.4801 (tp) outliers start: 40 outliers final: 27 residues processed: 181 average time/residue: 0.5091 time to fit residues: 98.3713 Evaluate side-chains 181 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 310 ILE 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 201 VAL Chi-restraints excluded: chain B residue 218 VAL 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 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 219 ARG 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 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 55 optimal weight: 0.1980 chunk 92 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 106 optimal weight: 0.0270 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.208225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152093 restraints weight = 9964.707| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.16 r_work: 0.3592 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8573 Z= 0.113 Angle : 0.608 12.501 11673 Z= 0.309 Chirality : 0.043 0.173 1376 Planarity : 0.004 0.053 1489 Dihedral : 5.338 59.119 1218 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.00 % Allowed : 24.82 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.68 (0.25), residues: 1120 helix: -0.77 (0.28), residues: 359 sheet: -0.98 (0.31), residues: 259 loop : -1.30 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 304 TYR 0.011 0.001 TYR E 190 PHE 0.034 0.001 PHE C 241 TRP 0.011 0.001 TRP C 82 HIS 0.004 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 8567) covalent geometry : angle 0.60684 / 0.31 (11660) SS BOND : bond 0.00754 / 0.37 ( 5) SS BOND : angle 1.44196 / 0.85 ( 10) hydrogen bonds : bond 0.02813 / 1.93 ( 289) hydrogen bonds : angle 4.79121 / 3.31 ( 795) link_TRANS : bond 0.00181 / 0.10 ( 1) link_TRANS : angle 0.86684 / 0.47 ( 3) *********************** 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 193 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.322 Fit side-chains REVERT: A 122 ASP cc_start: 0.5896 (m-30) cc_final: 0.5590 (t70) REVERT: A 180 TYR cc_start: 0.7187 (m-80) cc_final: 0.6551 (m-10) REVERT: A 218 LEU cc_start: 0.7231 (mm) cc_final: 0.6942 (tp) REVERT: B 9 ASP cc_start: 0.8285 (m-30) cc_final: 0.7771 (m-30) REVERT: B 21 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7864 (mtt90) REVERT: B 24 ARG cc_start: 0.7820 (ttp-110) cc_final: 0.7290 (ttp-110) REVERT: B 262 THR cc_start: 0.8495 (p) cc_final: 0.8240 (t) REVERT: B 274 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5393 (p90) REVERT: B 308 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: C 175 GLN cc_start: 0.8189 (pt0) cc_final: 0.7609 (pp30) REVERT: C 275 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7981 (m) REVERT: C 325 MET cc_start: 0.8032 (tpp) cc_final: 0.7747 (mmt) REVERT: E 19 LYS cc_start: 0.8425 (tttp) cc_final: 0.7911 (tppp) REVERT: E 186 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7674 (tm-30) REVERT: E 214 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5003 (tp) REVERT: E 220 GLU cc_start: 0.7423 (mp0) cc_final: 0.6772 (mp0) outliers start: 34 outliers final: 20 residues processed: 182 average time/residue: 0.5028 time to fit residues: 97.9461 Evaluate side-chains 173 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 205 TYR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 311 LEU 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 218 VAL 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 4 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU 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 C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 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 = 0.4338 r_free = 0.4338 target = 0.207870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.151469 restraints weight = 9993.251| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.42 r_work: 0.3577 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8573 Z= 0.122 Angle : 0.624 11.841 11673 Z= 0.319 Chirality : 0.044 0.172 1376 Planarity : 0.004 0.053 1489 Dihedral : 5.296 56.233 1218 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.29 % Allowed : 26.12 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.25), residues: 1120 helix: -0.64 (0.28), residues: 362 sheet: -0.96 (0.30), residues: 269 loop : -1.33 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 304 TYR 0.012 0.001 TYR E 173 PHE 0.032 0.002 PHE C 241 TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 8567) covalent geometry : angle 0.62260 / 0.32 (11660) SS BOND : bond 0.00769 / 0.38 ( 5) SS BOND : angle 1.50592 / 0.87 ( 10) hydrogen bonds : bond 0.02811 / 1.92 ( 289) hydrogen bonds : angle 4.78839 / 3.29 ( 795) link_TRANS : bond 0.00127 / 0.07 ( 1) link_TRANS : angle 0.81931 / 0.45 ( 3) ********************** 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 175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.327 Fit side-chains REVERT: A 180 TYR cc_start: 0.7144 (m-80) cc_final: 0.6510 (m-10) REVERT: A 218 LEU cc_start: 0.7252 (mm) cc_final: 0.6961 (tp) REVERT: A 300 LEU cc_start: 0.8317 (tp) cc_final: 0.8019 (tt) REVERT: B 21 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7556 (mtm110) REVERT: B 24 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7127 (ttp-110) REVERT: B 274 PHE cc_start: 0.5924 (OUTLIER) cc_final: 0.5429 (p90) REVERT: B 308 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: C 175 GLN cc_start: 0.8036 (pt0) cc_final: 0.7602 (pp30) REVERT: C 275 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7887 (m) REVERT: C 325 MET cc_start: 0.7806 (tpp) cc_final: 0.7431 (mmt) REVERT: E 19 LYS cc_start: 0.8291 (tttp) cc_final: 0.7858 (tppp) REVERT: E 186 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7590 (tm-30) REVERT: E 214 LEU cc_start: 0.5614 (OUTLIER) cc_final: 0.4800 (tp) REVERT: E 220 GLU cc_start: 0.7497 (mp0) cc_final: 0.6899 (mp0) outliers start: 28 outliers final: 20 residues processed: 167 average time/residue: 0.5172 time to fit residues: 92.3257 Evaluate side-chains 169 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 311 LEU 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 218 VAL 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 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 213 VAL 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 C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6573 > 50: distance: 6 - 9: 29.490 distance: 9 - 10: 39.419 distance: 10 - 11: 13.269 distance: 10 - 13: 16.994 distance: 11 - 12: 14.556 distance: 11 - 16: 35.079 distance: 13 - 14: 40.177 distance: 13 - 15: 14.300 distance: 16 - 17: 12.858 distance: 17 - 18: 39.272 distance: 17 - 20: 55.276 distance: 18 - 19: 41.648 distance: 18 - 22: 38.637 distance: 20 - 21: 39.298 distance: 22 - 23: 22.209 distance: 23 - 24: 22.852 distance: 23 - 26: 32.480 distance: 24 - 25: 48.089 distance: 24 - 28: 43.356 distance: 26 - 27: 38.199 distance: 28 - 29: 53.319 distance: 28 - 118: 25.537 distance: 29 - 30: 54.679 distance: 29 - 32: 67.657 distance: 30 - 31: 35.277 distance: 30 - 35: 60.958 distance: 32 - 33: 45.019 distance: 32 - 34: 14.511 distance: 35 - 36: 28.607 distance: 35 - 41: 50.664 distance: 36 - 37: 28.718 distance: 36 - 39: 32.198 distance: 37 - 38: 29.904 distance: 37 - 42: 22.698 distance: 39 - 40: 26.442 distance: 40 - 41: 39.833 distance: 42 - 43: 28.562 distance: 43 - 44: 38.605 distance: 43 - 46: 15.425 distance: 44 - 45: 55.793 distance: 44 - 49: 30.236 distance: 46 - 47: 22.603 distance: 46 - 48: 31.167 distance: 49 - 50: 37.812 distance: 50 - 51: 41.046 distance: 50 - 53: 42.748 distance: 51 - 52: 45.977 distance: 51 - 56: 41.582 distance: 53 - 54: 28.098 distance: 53 - 55: 32.042 distance: 56 - 57: 33.139 distance: 56 - 62: 32.622 distance: 57 - 58: 10.169 distance: 57 - 60: 22.180 distance: 58 - 59: 46.078 distance: 58 - 63: 44.901 distance: 60 - 61: 32.775 distance: 61 - 62: 16.330 distance: 63 - 64: 34.749 distance: 64 - 65: 40.947 distance: 65 - 66: 21.792 distance: 65 - 67: 42.292 distance: 67 - 68: 38.403 distance: 68 - 69: 21.803 distance: 68 - 71: 6.893 distance: 69 - 70: 18.864 distance: 69 - 76: 20.020 distance: 71 - 72: 20.181 distance: 72 - 73: 31.225 distance: 73 - 74: 30.857 distance: 73 - 75: 19.105