Starting phenix.real_space_refine on Sat Jul 26 06:28:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xav_33100/07_2025/7xav_33100.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xav_33100/07_2025/7xav_33100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2025/7xav_33100.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2025/7xav_33100.map" model { file = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2025/7xav_33100.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xav_33100/07_2025/7xav_33100.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.128 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5319 2.51 5 N 1436 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8410 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1896 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 11, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 184 Chain: "B" Number of atoms: 1602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1602 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Classifications: {'peptide': 4} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 6.75, per 1000 atoms: 0.80 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: 3.02 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.43 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: 4.18 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2544 1.33 - 1.46: 2293 1.46 - 1.59: 3655 1.59 - 1.72: 0 1.72 - 1.85: 75 Bond restraints: 8567 Sorted by residual: bond pdb=" CB VAL C 112 " pdb=" CG2 VAL C 112 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 7.02e+00 bond pdb=" CG1 ILE C 338 " pdb=" CD1 ILE C 338 " ideal model delta sigma weight residual 1.513 1.415 0.098 3.90e-02 6.57e+02 6.35e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.46e+00 bond pdb=" CA SER B 16 " pdb=" CB SER B 16 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.74e-02 3.30e+03 5.10e+00 bond pdb=" CB CYS C 317 " pdb=" SG CYS C 317 " ideal model delta sigma weight residual 1.808 1.737 0.071 3.30e-02 9.18e+02 4.65e+00 ... (remaining 8562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 11490 3.53 - 7.07: 150 7.07 - 10.60: 19 10.60 - 14.14: 0 14.14 - 17.67: 1 Bond angle restraints: 11660 Sorted by residual: angle pdb=" C THR B 190 " pdb=" N PHE B 191 " pdb=" CA PHE B 191 " ideal model delta sigma weight residual 122.58 114.37 8.21 2.07e+00 2.33e-01 1.57e+01 angle pdb=" C ASP C 246 " pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 121.52 130.50 -8.98 2.34e+00 1.83e-01 1.47e+01 angle pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta sigma weight residual 125.66 132.54 -6.88 1.85e+00 2.92e-01 1.38e+01 angle pdb=" C ASN C 88 " pdb=" CA ASN C 88 " pdb=" CB ASN C 88 " ideal model delta sigma weight residual 109.38 115.72 -6.34 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 121.54 128.02 -6.48 1.91e+00 2.74e-01 1.15e+01 ... (remaining 11655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 4441 15.39 - 30.77: 480 30.77 - 46.15: 118 46.15 - 61.54: 24 61.54 - 76.92: 7 Dihedral angle restraints: 5070 sinusoidal: 1769 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 161.80 -68.80 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS F 2 " pdb=" SG CYS F 2 " pdb=" SG CYS F 7 " pdb=" CB CYS F 7 " ideal model delta sinusoidal sigma weight residual -86.00 -31.70 -54.30 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 193 " pdb=" CB CYS A 193 " ideal model delta sinusoidal sigma weight residual -86.00 -33.81 -52.19 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 5067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 911 0.054 - 0.108: 342 0.108 - 0.162: 90 0.162 - 0.216: 24 0.216 - 0.270: 9 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CB VAL B 218 " pdb=" CA VAL B 218 " pdb=" CG1 VAL B 218 " pdb=" CG2 VAL B 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA CYS F 2 " pdb=" N CYS F 2 " pdb=" C CYS F 2 " pdb=" CB CYS F 2 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 145 " pdb=" CA VAL A 145 " pdb=" CG1 VAL A 145 " pdb=" CG2 VAL A 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1373 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.87e+00 pdb=" N PRO A 176 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 319 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C ILE B 319 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE B 319 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR B 320 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 151 " -0.029 2.00e-02 2.50e+03 1.99e-02 6.92e+00 pdb=" CG PHE C 151 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 151 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE C 151 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 151 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 151 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 151 " -0.007 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.18: 1 2.18 - 2.86: 3112 2.86 - 3.54: 10857 3.54 - 4.22: 20826 4.22 - 4.90: 35098 Nonbonded interactions: 69894 Sorted by model distance: nonbonded pdb=" CG2 THR A 212 " pdb=" CZ3 DTR F 4 " model vdw 1.494 3.760 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.181 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.240 3.040 nonbonded pdb=" O ASP E 223 " pdb=" OH TYR E 227 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O GLY C 288 " model vdw 2.252 3.040 ... (remaining 69889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 71.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.110 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:151.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 253.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.098 8573 Z= 0.398 Angle : 1.053 17.673 11673 Z= 0.568 Chirality : 0.064 0.270 1376 Planarity : 0.007 0.079 1489 Dihedral : 14.144 76.924 2920 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 0.71 % Allowed : 10.12 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.20), residues: 1120 helix: -4.55 (0.13), residues: 343 sheet: -1.92 (0.30), residues: 257 loop : -2.53 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 99 HIS 0.008 0.002 HIS C 91 PHE 0.042 0.004 PHE C 151 TYR 0.035 0.003 TYR C 105 ARG 0.006 0.001 ARG B 21 Details of bonding type rmsd link_TRANS : bond 0.00501 ( 1) link_TRANS : angle 0.28799 ( 3) hydrogen bonds : bond 0.29973 ( 289) hydrogen bonds : angle 11.03237 ( 795) SS BOND : bond 0.01405 ( 5) SS BOND : angle 2.55916 ( 10) covalent geometry : bond 0.00915 ( 8567) covalent geometry : angle 1.05126 (11660) *********************** 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 : 1.141 Fit side-chains REVERT: A 122 ASP cc_start: 0.6663 (m-30) cc_final: 0.6403 (m-30) REVERT: A 173 VAL cc_start: 0.8208 (t) cc_final: 0.7973 (p) REVERT: A 180 TYR cc_start: 0.7658 (m-80) cc_final: 0.7038 (m-80) REVERT: A 196 ASN cc_start: 0.7340 (m110) cc_final: 0.7107 (m110) REVERT: B 24 ARG cc_start: 0.7468 (ttp-110) cc_final: 0.7040 (ttp-110) REVERT: B 262 THR cc_start: 0.8514 (p) cc_final: 0.8314 (p) REVERT: B 333 GLN cc_start: 0.8052 (tp40) cc_final: 0.7360 (tp40) REVERT: C 154 ASP cc_start: 0.7530 (m-30) cc_final: 0.7283 (m-30) REVERT: C 175 GLN cc_start: 0.7974 (pt0) cc_final: 0.7555 (pp30) REVERT: C 215 GLU cc_start: 0.7278 (tp30) cc_final: 0.6693 (tp30) REVERT: E 19 LYS cc_start: 0.8430 (tttp) cc_final: 0.8096 (tppp) REVERT: E 38 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7772 (ptp-170) outliers start: 6 outliers final: 2 residues processed: 187 average time/residue: 1.1943 time to fit residues: 238.2639 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 : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN B 188 HIS B 346 ASN B 347 ASN C 62 HIS C 239 ASN E 39 GLN E 113 GLN E 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.204039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147621 restraints weight = 9855.319| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.51 r_work: 0.3498 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8573 Z= 0.183 Angle : 0.685 12.382 11673 Z= 0.359 Chirality : 0.045 0.236 1376 Planarity : 0.005 0.057 1489 Dihedral : 6.330 37.657 1219 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.53 % Allowed : 16.59 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.22), residues: 1120 helix: -3.37 (0.19), residues: 365 sheet: -1.75 (0.29), residues: 280 loop : -2.04 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 99 HIS 0.005 0.001 HIS C 91 PHE 0.019 0.002 PHE C 151 TYR 0.019 0.002 TYR C 59 ARG 0.006 0.001 ARG E 160 Details of bonding type rmsd link_TRANS : bond 0.00504 ( 1) link_TRANS : angle 0.35557 ( 3) hydrogen bonds : bond 0.04605 ( 289) hydrogen bonds : angle 6.33610 ( 795) SS BOND : bond 0.00862 ( 5) SS BOND : angle 1.65735 ( 10) covalent geometry : bond 0.00412 ( 8567) covalent geometry : angle 0.68408 (11660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.505 Fit side-chains REVERT: A 93 MET cc_start: 0.6872 (mmm) cc_final: 0.6633 (tpt) REVERT: A 122 ASP cc_start: 0.6693 (m-30) cc_final: 0.6225 (t0) REVERT: A 196 ASN cc_start: 0.7359 (m110) cc_final: 0.7015 (m110) REVERT: A 209 ILE cc_start: 0.7511 (pt) cc_final: 0.7297 (mp) REVERT: A 302 TYR cc_start: 0.8009 (m-80) cc_final: 0.7745 (m-80) REVERT: B 24 ARG cc_start: 0.7648 (ttp-110) cc_final: 0.6997 (ttp-110) REVERT: B 262 THR cc_start: 0.8569 (p) cc_final: 0.8289 (t) REVERT: C 154 ASP cc_start: 0.7793 (m-30) cc_final: 0.7482 (m-30) REVERT: C 175 GLN cc_start: 0.8310 (pt0) cc_final: 0.7609 (pp30) REVERT: E 19 LYS cc_start: 0.8494 (tttp) cc_final: 0.8023 (tppp) REVERT: E 234 GLU cc_start: 0.8225 (pt0) cc_final: 0.7774 (pt0) outliers start: 30 outliers final: 12 residues processed: 195 average time/residue: 1.4036 time to fit residues: 294.3236 Evaluate side-chains 167 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.206302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.150115 restraints weight = 9948.503| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.15 r_work: 0.3557 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8573 Z= 0.132 Angle : 0.614 12.580 11673 Z= 0.318 Chirality : 0.044 0.163 1376 Planarity : 0.004 0.054 1489 Dihedral : 5.776 40.551 1219 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.94 % Allowed : 18.94 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.23), residues: 1120 helix: -2.51 (0.23), residues: 363 sheet: -1.42 (0.28), residues: 283 loop : -1.83 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 91 PHE 0.018 0.001 PHE C 241 TYR 0.016 0.002 TYR A 180 ARG 0.005 0.000 ARG E 160 Details of bonding type rmsd link_TRANS : bond 0.00225 ( 1) link_TRANS : angle 0.19586 ( 3) hydrogen bonds : bond 0.03545 ( 289) hydrogen bonds : angle 5.57492 ( 795) SS BOND : bond 0.00685 ( 5) SS BOND : angle 1.82503 ( 10) covalent geometry : bond 0.00291 ( 8567) covalent geometry : angle 0.61216 (11660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6415 (m-30) cc_final: 0.5967 (t0) REVERT: A 180 TYR cc_start: 0.7317 (m-80) cc_final: 0.6754 (m-10) REVERT: A 196 ASN cc_start: 0.7376 (m110) cc_final: 0.7153 (m110) REVERT: A 302 TYR cc_start: 0.8184 (m-80) cc_final: 0.7908 (m-80) REVERT: B 9 ASP cc_start: 0.8298 (m-30) cc_final: 0.7871 (m-30) REVERT: B 24 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7276 (ttp-110) REVERT: B 262 THR cc_start: 0.8545 (p) cc_final: 0.8239 (t) REVERT: B 274 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.5457 (p90) REVERT: C 175 GLN cc_start: 0.8404 (pt0) cc_final: 0.7725 (pp30) REVERT: C 275 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.8014 (m) REVERT: C 325 MET cc_start: 0.7995 (tpp) cc_final: 0.7640 (mmt) REVERT: E 13 GLN cc_start: 0.7328 (pp30) cc_final: 0.7022 (pp30) REVERT: E 19 LYS cc_start: 0.8473 (tttp) cc_final: 0.7934 (tppp) REVERT: E 76 LYS cc_start: 0.8061 (mptt) cc_final: 0.7841 (mttp) REVERT: E 234 GLU cc_start: 0.8398 (pt0) cc_final: 0.8072 (pt0) outliers start: 42 outliers final: 19 residues processed: 191 average time/residue: 1.1283 time to fit residues: 230.7759 Evaluate side-chains 168 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 75 GLN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151134 restraints weight = 9947.228| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.15 r_work: 0.3573 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8573 Z= 0.118 Angle : 0.595 12.294 11673 Z= 0.305 Chirality : 0.043 0.179 1376 Planarity : 0.004 0.052 1489 Dihedral : 5.358 43.585 1219 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.71 % Allowed : 20.47 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.24), residues: 1120 helix: -1.98 (0.25), residues: 364 sheet: -1.34 (0.28), residues: 293 loop : -1.66 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.011 0.001 PHE B 334 TYR 0.012 0.001 TYR E 103 ARG 0.009 0.000 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00051 ( 1) link_TRANS : angle 0.20695 ( 3) hydrogen bonds : bond 0.03109 ( 289) hydrogen bonds : angle 5.08044 ( 795) SS BOND : bond 0.00946 ( 5) SS BOND : angle 1.80211 ( 10) covalent geometry : bond 0.00259 ( 8567) covalent geometry : angle 0.59252 (11660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.6177 (m-30) cc_final: 0.5812 (t70) REVERT: A 180 TYR cc_start: 0.7293 (m-80) cc_final: 0.6646 (m-10) REVERT: A 302 TYR cc_start: 0.8048 (m-80) cc_final: 0.7844 (m-80) REVERT: B 9 ASP cc_start: 0.8355 (m-30) cc_final: 0.7903 (m-30) REVERT: B 21 ARG cc_start: 0.8215 (ptp90) cc_final: 0.7756 (mtm110) REVERT: B 24 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7308 (ttp-110) REVERT: B 262 THR cc_start: 0.8464 (p) cc_final: 0.8263 (t) REVERT: C 175 GLN cc_start: 0.8203 (pt0) cc_final: 0.7584 (pp30) REVERT: C 234 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: C 275 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (m) REVERT: C 325 MET cc_start: 0.7997 (tpp) cc_final: 0.7642 (mmt) REVERT: E 19 LYS cc_start: 0.8449 (tttp) cc_final: 0.7896 (tppp) REVERT: E 189 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7793 (mp) REVERT: E 234 GLU cc_start: 0.8411 (pt0) cc_final: 0.8138 (pt0) outliers start: 40 outliers final: 18 residues processed: 191 average time/residue: 1.0835 time to fit residues: 221.7523 Evaluate side-chains 170 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 237 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154500 restraints weight = 9900.525| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.53 r_work: 0.3550 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8573 Z= 0.121 Angle : 0.585 12.251 11673 Z= 0.302 Chirality : 0.043 0.190 1376 Planarity : 0.004 0.050 1489 Dihedral : 5.228 47.078 1219 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.59 % Allowed : 22.71 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.24), residues: 1120 helix: -1.59 (0.26), residues: 368 sheet: -1.12 (0.30), residues: 264 loop : -1.61 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.031 0.002 PHE B 189 TYR 0.013 0.001 TYR E 173 ARG 0.007 0.000 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00041 ( 1) link_TRANS : angle 0.40311 ( 3) hydrogen bonds : bond 0.02977 ( 289) hydrogen bonds : angle 4.95339 ( 795) SS BOND : bond 0.00931 ( 5) SS BOND : angle 1.58720 ( 10) covalent geometry : bond 0.00270 ( 8567) covalent geometry : angle 0.58330 (11660) *********************** 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 187 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 122 ASP cc_start: 0.5905 (m-30) cc_final: 0.5524 (t0) REVERT: A 180 TYR cc_start: 0.7169 (m-80) cc_final: 0.6468 (m-10) REVERT: A 218 LEU cc_start: 0.7205 (mm) cc_final: 0.6865 (tp) REVERT: B 21 ARG cc_start: 0.8010 (ptp90) cc_final: 0.7582 (mtm110) REVERT: B 24 ARG cc_start: 0.7720 (ttp-110) cc_final: 0.7122 (ttp-110) REVERT: B 308 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: C 175 GLN cc_start: 0.8105 (pt0) cc_final: 0.7505 (pp30) REVERT: C 275 SER cc_start: 0.8098 (OUTLIER) cc_final: 0.7764 (m) REVERT: C 325 MET cc_start: 0.7878 (tpp) cc_final: 0.7492 (mmt) REVERT: D 47 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6211 (pm20) REVERT: E 19 LYS cc_start: 0.8439 (tttp) cc_final: 0.7927 (tppp) REVERT: E 186 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7519 (tm-30) outliers start: 39 outliers final: 21 residues processed: 173 average time/residue: 1.5256 time to fit residues: 282.2506 Evaluate side-chains 166 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 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 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 99 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.207062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150425 restraints weight = 9890.789| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.17 r_work: 0.3575 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8573 Z= 0.125 Angle : 0.583 11.855 11673 Z= 0.302 Chirality : 0.043 0.177 1376 Planarity : 0.004 0.050 1489 Dihedral : 5.185 50.829 1219 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.94 % Allowed : 22.24 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.25), residues: 1120 helix: -1.21 (0.27), residues: 362 sheet: -0.97 (0.30), residues: 273 loop : -1.46 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 99 HIS 0.003 0.001 HIS C 91 PHE 0.026 0.002 PHE B 189 TYR 0.012 0.001 TYR E 103 ARG 0.009 0.000 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.40640 ( 3) hydrogen bonds : bond 0.02950 ( 289) hydrogen bonds : angle 4.86427 ( 795) SS BOND : bond 0.00861 ( 5) SS BOND : angle 1.51871 ( 10) covalent geometry : bond 0.00283 ( 8567) covalent geometry : angle 0.58133 (11660) *********************** 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 198 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7608 (m-40) cc_final: 0.7361 (m-40) REVERT: A 122 ASP cc_start: 0.6320 (m-30) cc_final: 0.5851 (t70) REVERT: A 180 TYR cc_start: 0.7198 (m-80) cc_final: 0.6405 (m-10) REVERT: A 218 LEU cc_start: 0.7245 (mm) cc_final: 0.6924 (tp) REVERT: B 21 ARG cc_start: 0.8199 (ptp90) cc_final: 0.7812 (mtm110) REVERT: B 24 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7349 (ttp-110) REVERT: B 308 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: C 175 GLN cc_start: 0.8199 (pt0) cc_final: 0.7613 (pp30) REVERT: C 275 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7916 (m) REVERT: C 325 MET cc_start: 0.8061 (tpp) cc_final: 0.7709 (mmt) REVERT: D 62 ARG cc_start: 0.5756 (mtm110) cc_final: 0.5554 (mtt90) REVERT: E 19 LYS cc_start: 0.8435 (tttp) cc_final: 0.7914 (tppp) REVERT: E 160 ARG cc_start: 0.6462 (mmm160) cc_final: 0.6199 (mmm160) REVERT: E 186 GLN cc_start: 0.7910 (tm-30) cc_final: 0.7649 (tm-30) REVERT: E 189 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7898 (mp) outliers start: 42 outliers final: 28 residues processed: 184 average time/residue: 1.4064 time to fit residues: 275.3082 Evaluate side-chains 178 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 273 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 47 GLU 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 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151974 restraints weight = 9970.017| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.55 r_work: 0.3539 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8573 Z= 0.127 Angle : 0.595 11.971 11673 Z= 0.307 Chirality : 0.043 0.181 1376 Planarity : 0.004 0.050 1489 Dihedral : 5.151 54.323 1219 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.41 % Allowed : 23.06 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.25), residues: 1120 helix: -1.01 (0.27), residues: 363 sheet: -0.80 (0.31), residues: 266 loop : -1.40 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.025 0.002 PHE C 241 TYR 0.027 0.002 TYR A 205 ARG 0.011 0.000 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00164 ( 1) link_TRANS : angle 0.56174 ( 3) hydrogen bonds : bond 0.02924 ( 289) hydrogen bonds : angle 4.84446 ( 795) SS BOND : bond 0.00869 ( 5) SS BOND : angle 1.58337 ( 10) covalent geometry : bond 0.00288 ( 8567) covalent geometry : angle 0.59313 (11660) *********************** 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 199 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7793 (mm) cc_final: 0.7583 (tp) REVERT: A 61 ASN cc_start: 0.7532 (m-40) cc_final: 0.7302 (m-40) REVERT: A 122 ASP cc_start: 0.5924 (m-30) cc_final: 0.5490 (t0) REVERT: A 180 TYR cc_start: 0.7132 (m-80) cc_final: 0.6436 (m-10) REVERT: A 218 LEU cc_start: 0.7263 (mm) cc_final: 0.6957 (tp) REVERT: A 248 LYS cc_start: 0.5544 (tppp) cc_final: 0.5256 (mppt) REVERT: B 21 ARG cc_start: 0.7984 (ptp90) cc_final: 0.7629 (mtm110) REVERT: B 24 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7161 (ttp-110) REVERT: B 308 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: C 175 GLN cc_start: 0.8132 (pt0) cc_final: 0.7580 (pp30) REVERT: C 275 SER cc_start: 0.8088 (OUTLIER) cc_final: 0.7747 (m) REVERT: C 325 MET cc_start: 0.7895 (tpp) cc_final: 0.7530 (mmt) REVERT: E 19 LYS cc_start: 0.8320 (tttp) cc_final: 0.7887 (tppp) REVERT: E 186 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7572 (tm-30) REVERT: E 189 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7763 (mp) outliers start: 46 outliers final: 29 residues processed: 183 average time/residue: 1.6803 time to fit residues: 328.1003 Evaluate side-chains 179 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 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 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 308 ASN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.206758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.149483 restraints weight = 9938.050| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.19 r_work: 0.3562 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8573 Z= 0.137 Angle : 0.600 11.570 11673 Z= 0.312 Chirality : 0.044 0.167 1376 Planarity : 0.004 0.050 1489 Dihedral : 5.181 55.725 1219 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.82 % Allowed : 24.12 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.25), residues: 1120 helix: -0.76 (0.28), residues: 358 sheet: -0.89 (0.30), residues: 273 loop : -1.32 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 99 HIS 0.003 0.001 HIS C 91 PHE 0.028 0.002 PHE C 241 TYR 0.013 0.001 TYR E 103 ARG 0.010 0.001 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00099 ( 1) link_TRANS : angle 0.57561 ( 3) hydrogen bonds : bond 0.02964 ( 289) hydrogen bonds : angle 4.86487 ( 795) SS BOND : bond 0.00926 ( 5) SS BOND : angle 1.64832 ( 10) covalent geometry : bond 0.00312 ( 8567) covalent geometry : angle 0.59865 (11660) *********************** 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 197 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7639 (m-40) cc_final: 0.7352 (m-40) REVERT: A 122 ASP cc_start: 0.6167 (m-30) cc_final: 0.5678 (t0) REVERT: A 180 TYR cc_start: 0.7193 (m-80) cc_final: 0.6507 (m-10) REVERT: A 218 LEU cc_start: 0.7337 (mm) cc_final: 0.7001 (tp) REVERT: A 248 LYS cc_start: 0.5594 (tppp) cc_final: 0.5209 (mppt) REVERT: B 21 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7810 (mtm110) REVERT: B 24 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.7284 (ttp-110) REVERT: B 308 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: C 175 GLN cc_start: 0.8205 (pt0) cc_final: 0.7597 (pp30) REVERT: C 275 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7841 (m) REVERT: C 325 MET cc_start: 0.8060 (tpp) cc_final: 0.7711 (mmt) REVERT: E 19 LYS cc_start: 0.8342 (tttp) cc_final: 0.7894 (tppp) REVERT: E 43 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7275 (tppp) REVERT: E 83 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6930 (ptm) REVERT: E 186 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 189 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7782 (mp) REVERT: E 214 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.4842 (tp) REVERT: E 220 GLU cc_start: 0.7432 (mp0) cc_final: 0.6780 (mp0) outliers start: 41 outliers final: 33 residues processed: 183 average time/residue: 1.0354 time to fit residues: 203.4834 Evaluate side-chains 189 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 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 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 243 MET Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 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 234 PHE Chi-restraints excluded: chain C residue 273 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 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE 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 90 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 79 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 15 optimal weight: 50.0000 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.205694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147685 restraints weight = 10035.980| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.23 r_work: 0.3546 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8573 Z= 0.162 Angle : 0.627 11.657 11673 Z= 0.326 Chirality : 0.045 0.180 1376 Planarity : 0.004 0.051 1489 Dihedral : 5.271 56.258 1219 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.06 % Allowed : 24.24 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.25), residues: 1120 helix: -0.72 (0.28), residues: 359 sheet: -0.98 (0.30), residues: 275 loop : -1.34 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS C 91 PHE 0.037 0.002 PHE C 241 TYR 0.014 0.002 TYR E 103 ARG 0.009 0.001 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.51056 ( 3) hydrogen bonds : bond 0.03110 ( 289) hydrogen bonds : angle 4.95148 ( 795) SS BOND : bond 0.01049 ( 5) SS BOND : angle 1.73914 ( 10) covalent geometry : bond 0.00374 ( 8567) covalent geometry : angle 0.62524 (11660) *********************** 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 192 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7700 (m-40) cc_final: 0.7386 (m-40) REVERT: A 122 ASP cc_start: 0.6178 (m-30) cc_final: 0.5658 (t0) REVERT: A 218 LEU cc_start: 0.7361 (mm) cc_final: 0.7014 (tp) REVERT: A 248 LYS cc_start: 0.5645 (tppp) cc_final: 0.5260 (mppt) REVERT: B 21 ARG cc_start: 0.8171 (ptp90) cc_final: 0.7805 (mtm110) REVERT: B 24 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.7251 (ttp-110) REVERT: B 308 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: C 175 GLN cc_start: 0.8243 (pt0) cc_final: 0.7628 (pp30) REVERT: C 275 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7830 (m) REVERT: C 325 MET cc_start: 0.8074 (tpp) cc_final: 0.7648 (mmt) REVERT: E 19 LYS cc_start: 0.8360 (tttp) cc_final: 0.7917 (tppp) REVERT: E 43 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7286 (tppp) REVERT: E 82 GLN cc_start: 0.7224 (tp-100) cc_final: 0.6991 (tp40) REVERT: E 83 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6990 (ptm) REVERT: E 160 ARG cc_start: 0.6515 (mmm160) cc_final: 0.6211 (mmm160) REVERT: E 186 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7660 (tm-30) REVERT: E 189 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7778 (mp) REVERT: E 214 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.4934 (tp) REVERT: E 220 GLU cc_start: 0.7435 (mp0) cc_final: 0.6816 (mp0) outliers start: 43 outliers final: 31 residues processed: 179 average time/residue: 1.0782 time to fit residues: 206.6732 Evaluate side-chains 185 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 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 219 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 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 43 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 189 ILE 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 44 optimal weight: 10.0000 chunk 12 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.207322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152532 restraints weight = 9902.312| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.38 r_work: 0.3556 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8573 Z= 0.133 Angle : 0.632 11.686 11673 Z= 0.323 Chirality : 0.044 0.162 1376 Planarity : 0.004 0.062 1489 Dihedral : 5.199 59.096 1219 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.24 % Allowed : 25.06 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.25), residues: 1120 helix: -0.56 (0.28), residues: 359 sheet: -0.87 (0.31), residues: 270 loop : -1.35 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 47 HIS 0.004 0.001 HIS C 91 PHE 0.033 0.002 PHE C 241 TYR 0.012 0.001 TYR A 211 ARG 0.014 0.001 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00130 ( 1) link_TRANS : angle 0.51641 ( 3) hydrogen bonds : bond 0.02907 ( 289) hydrogen bonds : angle 4.83680 ( 795) SS BOND : bond 0.00864 ( 5) SS BOND : angle 1.54691 ( 10) covalent geometry : bond 0.00301 ( 8567) covalent geometry : angle 0.63115 (11660) ********************** 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 183 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7572 (m-40) cc_final: 0.7322 (m-40) REVERT: A 218 LEU cc_start: 0.7276 (mm) cc_final: 0.6926 (tp) REVERT: A 248 LYS cc_start: 0.5640 (tppp) cc_final: 0.5308 (mppt) REVERT: B 21 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7568 (mtm110) REVERT: B 24 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7088 (ttp-110) REVERT: B 308 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: C 175 GLN cc_start: 0.8087 (pt0) cc_final: 0.7508 (pp30) REVERT: C 275 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7585 (m) REVERT: C 325 MET cc_start: 0.7864 (tpp) cc_final: 0.7483 (mmt) REVERT: E 19 LYS cc_start: 0.8302 (tttp) cc_final: 0.7835 (tppp) REVERT: E 76 LYS cc_start: 0.8304 (mptt) cc_final: 0.7836 (ptpt) REVERT: E 186 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7507 (tm-30) REVERT: E 189 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7603 (mp) REVERT: E 214 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.4862 (tp) REVERT: E 220 GLU cc_start: 0.7447 (mp0) cc_final: 0.6865 (mp0) outliers start: 36 outliers final: 26 residues processed: 172 average time/residue: 1.0978 time to fit residues: 201.8578 Evaluate side-chains 175 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 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 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 47 GLU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 189 ILE 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 3 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 0.0040 chunk 35 optimal weight: 0.0770 chunk 13 optimal weight: 0.0000 chunk 49 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 108 optimal weight: 7.9990 overall best weight: 0.1332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.212480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.158251 restraints weight = 10051.267| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.16 r_work: 0.3678 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8573 Z= 0.102 Angle : 0.583 11.261 11673 Z= 0.302 Chirality : 0.042 0.161 1376 Planarity : 0.004 0.055 1489 Dihedral : 4.863 51.196 1219 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.41 % Allowed : 25.88 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.26), residues: 1120 helix: -0.36 (0.29), residues: 364 sheet: -0.68 (0.31), residues: 265 loop : -1.33 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.002 0.000 HIS E 35 PHE 0.026 0.001 PHE C 241 TYR 0.025 0.001 TYR A 205 ARG 0.014 0.001 ARG C 304 Details of bonding type rmsd link_TRANS : bond 0.00187 ( 1) link_TRANS : angle 0.59278 ( 3) hydrogen bonds : bond 0.02483 ( 289) hydrogen bonds : angle 4.61108 ( 795) SS BOND : bond 0.00556 ( 5) SS BOND : angle 1.07043 ( 10) covalent geometry : bond 0.00221 ( 8567) covalent geometry : angle 0.58203 (11660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9649.87 seconds wall clock time: 174 minutes 4.58 seconds (10444.58 seconds total)