Starting phenix.real_space_refine on Sun Aug 24 06:20:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsj_34999/08_2025/8hsj_34999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsj_34999/08_2025/8hsj_34999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hsj_34999/08_2025/8hsj_34999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsj_34999/08_2025/8hsj_34999.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsj_34999/08_2025/8hsj_34999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsj_34999/08_2025/8hsj_34999.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 42 5.16 5 Be 6 3.05 5 C 10800 2.51 5 N 3132 2.21 5 O 3228 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17244 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "B" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "D" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "E" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "F" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2842 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 341} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.85, per 1000 atoms: 0.22 Number of scatterers: 17244 At special positions: 0 Unit cell: (136.74, 130.38, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 42 16.00 P 12 15.00 Mg 6 11.99 F 18 9.00 O 3228 8.00 N 3132 7.00 C 10800 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 740.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 23 sheets defined 46.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 91 through 99 removed outlier: 4.332A pdb=" N ILE A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.565A pdb=" N LYS A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.627A pdb=" N HIS A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.769A pdb=" N ASP A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.670A pdb=" N LEU A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 395 Processing helix chain 'A' and resid 398 through 411 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'B' and resid 91 through 99 removed outlier: 4.204A pdb=" N ILE B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.515A pdb=" N ALA B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 137' Processing helix chain 'B' and resid 141 through 145 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 190 through 205 removed outlier: 3.512A pdb=" N LYS B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 229 Processing helix chain 'B' and resid 242 through 262 removed outlier: 3.533A pdb=" N HIS B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 332 through 344 removed outlier: 3.835A pdb=" N ASP B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 344 " --> pdb=" O GLU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.580A pdb=" N LEU B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 395 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'C' and resid 91 through 99 removed outlier: 4.157A pdb=" N ILE C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.637A pdb=" N ALA C 136 " --> pdb=" O ASP C 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.579A pdb=" N LYS C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 242 through 262 removed outlier: 3.524A pdb=" N HIS C 246 " --> pdb=" O PRO C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 301 through 310 Processing helix chain 'C' and resid 332 through 344 removed outlier: 3.785A pdb=" N ASP C 336 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 359 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.581A pdb=" N LEU C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.811A pdb=" N ALA C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'D' and resid 91 through 99 removed outlier: 4.100A pdb=" N ILE D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 removed outlier: 3.543A pdb=" N LYS D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.529A pdb=" N LYS D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 242 through 262 removed outlier: 3.602A pdb=" N HIS D 246 " --> pdb=" O PRO D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 301 through 310 Processing helix chain 'D' and resid 332 through 344 removed outlier: 3.797A pdb=" N ASP D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.689A pdb=" N LEU D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 395 Processing helix chain 'D' and resid 398 through 411 Processing helix chain 'D' and resid 414 through 420 Processing helix chain 'E' and resid 91 through 99 removed outlier: 4.515A pdb=" N ILE E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 141 through 145 Processing helix chain 'E' and resid 161 through 172 Processing helix chain 'E' and resid 190 through 205 removed outlier: 3.554A pdb=" N LYS E 203 " --> pdb=" O ASN E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 229 Processing helix chain 'E' and resid 242 through 262 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 301 through 310 Processing helix chain 'E' and resid 332 through 344 removed outlier: 3.800A pdb=" N ASP E 336 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 380 through 395 Processing helix chain 'E' and resid 398 through 411 Processing helix chain 'E' and resid 414 through 420 Processing helix chain 'F' and resid 91 through 99 removed outlier: 4.175A pdb=" N ILE F 95 " --> pdb=" O SER F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 161 through 172 Processing helix chain 'F' and resid 190 through 205 removed outlier: 3.573A pdb=" N LYS F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 229 Processing helix chain 'F' and resid 242 through 263 removed outlier: 3.553A pdb=" N HIS F 246 " --> pdb=" O PRO F 242 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 263 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 285 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 301 through 310 Processing helix chain 'F' and resid 332 through 344 removed outlier: 3.759A pdb=" N ASP F 336 " --> pdb=" O SER F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 359 Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.606A pdb=" N LEU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 394 Processing helix chain 'F' and resid 395 through 397 No H-bonds generated for 'chain 'F' and resid 395 through 397' Processing helix chain 'F' and resid 398 through 411 removed outlier: 3.658A pdb=" N ALA F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 420 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 7.124A pdb=" N GLN A 109 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.754A pdb=" N ASN A 313 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 267 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE A 269 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N LEU A 327 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 209 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A 268 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 215 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL A 210 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE A 235 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL A 212 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER A 237 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 214 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.754A pdb=" N ASN A 313 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY A 180 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA A 326 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 182 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 64 Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 148 removed outlier: 3.703A pdb=" N ASN B 313 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 209 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 215 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 210 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE B 235 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL B 212 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER B 237 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 214 " --> pdb=" O SER B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 147 through 148 removed outlier: 3.703A pdb=" N ASN B 313 " --> pdb=" O GLN B 148 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLY B 180 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ALA B 326 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 182 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 349 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 371 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 64 removed outlier: 7.716A pdb=" N GLN C 109 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 123 " --> pdb=" O GLN C 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AB2, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.791A pdb=" N ASN C 313 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C 209 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET C 268 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 215 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 210 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE C 235 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL C 212 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N SER C 237 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 214 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.791A pdb=" N ASN C 313 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLY C 180 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ALA C 326 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 182 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 62 through 65 Processing sheet with id=AB5, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AB6, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.724A pdb=" N ASN D 313 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL D 267 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N LEU D 323 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE D 269 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR D 325 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU D 271 " --> pdb=" O THR D 325 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N LEU D 327 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 215 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL D 210 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ILE D 235 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N VAL D 212 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER D 237 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 214 " --> pdb=" O SER D 237 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 147 through 148 removed outlier: 3.724A pdb=" N ASN D 313 " --> pdb=" O GLN D 148 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N GLY D 180 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ALA D 326 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE D 182 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 62 through 64 Processing sheet with id=AB9, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AC1, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.793A pdb=" N ASN E 313 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS E 209 " --> pdb=" O MET E 268 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU E 270 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE E 211 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ASP E 272 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU E 213 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL E 210 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE E 235 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL E 212 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER E 237 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 214 " --> pdb=" O SER E 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.793A pdb=" N ASN E 313 " --> pdb=" O GLN E 148 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLY E 180 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA E 326 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE E 182 " --> pdb=" O ALA E 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 88 through 90 Processing sheet with id=AC4, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.799A pdb=" N ASN F 313 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS F 209 " --> pdb=" O MET F 268 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU F 270 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE F 211 " --> pdb=" O LEU F 270 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ASP F 272 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 213 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL F 210 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE F 235 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL F 212 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N SER F 237 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU F 214 " --> pdb=" O SER F 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.799A pdb=" N ASN F 313 " --> pdb=" O GLN F 148 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLY F 180 " --> pdb=" O ALA F 324 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ALA F 326 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE F 182 " --> pdb=" O ALA F 326 " (cutoff:3.500A) 770 hydrogen bonds defined for protein. 2142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5908 1.34 - 1.46: 3223 1.46 - 1.58: 8275 1.58 - 1.69: 18 1.69 - 1.81: 84 Bond restraints: 17508 Sorted by residual: bond pdb=" F2 BEF C1002 " pdb="BE BEF C1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" F2 BEF B1002 " pdb="BE BEF B1002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F2 BEF D1002 " pdb="BE BEF D1002 " ideal model delta sigma weight residual 1.476 1.558 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" F2 BEF E1002 " pdb="BE BEF E1002 " ideal model delta sigma weight residual 1.476 1.557 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 17503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 23435 2.92 - 5.85: 222 5.85 - 8.77: 16 8.77 - 11.69: 9 11.69 - 14.61: 6 Bond angle restraints: 23688 Sorted by residual: angle pdb=" C ALA B 136 " pdb=" N LYS B 137 " pdb=" CA LYS B 137 " ideal model delta sigma weight residual 120.28 131.12 -10.84 1.44e+00 4.82e-01 5.66e+01 angle pdb=" OG1 THR A 288 " pdb=" CB THR A 288 " pdb=" CG2 THR A 288 " ideal model delta sigma weight residual 109.30 120.07 -10.77 2.00e+00 2.50e-01 2.90e+01 angle pdb=" CA THR A 288 " pdb=" CB THR A 288 " pdb=" CG2 THR A 288 " ideal model delta sigma weight residual 110.50 119.02 -8.52 1.70e+00 3.46e-01 2.51e+01 angle pdb=" F2 BEF C1002 " pdb="BE BEF C1002 " pdb=" F3 BEF C1002 " ideal model delta sigma weight residual 119.96 105.35 14.61 3.00e+00 1.11e-01 2.37e+01 angle pdb=" F2 BEF F1002 " pdb="BE BEF F1002 " pdb=" F3 BEF F1002 " ideal model delta sigma weight residual 119.96 107.18 12.78 3.00e+00 1.11e-01 1.81e+01 ... (remaining 23683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 10598 35.40 - 70.80: 210 70.80 - 106.20: 12 106.20 - 141.60: 6 141.60 - 177.00: 4 Dihedral angle restraints: 10830 sinusoidal: 4602 harmonic: 6228 Sorted by residual: dihedral pdb=" O1B ADP C1000 " pdb=" O3A ADP C1000 " pdb=" PB ADP C1000 " pdb=" PA ADP C1000 " ideal model delta sinusoidal sigma weight residual -60.00 117.00 -177.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D1000 " pdb=" O3A ADP D1000 " pdb=" PB ADP D1000 " pdb=" PA ADP D1000 " ideal model delta sinusoidal sigma weight residual 300.00 130.52 169.48 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP E1000 " pdb=" O3A ADP E1000 " pdb=" PB ADP E1000 " pdb=" PA ADP E1000 " ideal model delta sinusoidal sigma weight residual -60.00 85.53 -145.53 1 2.00e+01 2.50e-03 4.38e+01 ... (remaining 10827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 2716 0.270 - 0.539: 1 0.539 - 0.809: 0 0.809 - 1.079: 0 1.079 - 1.348: 1 Chirality restraints: 2718 Sorted by residual: chirality pdb=" CB THR A 288 " pdb=" CA THR A 288 " pdb=" OG1 THR A 288 " pdb=" CG2 THR A 288 " both_signs ideal model delta sigma weight residual False 2.55 1.20 1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA SER C 164 " pdb=" N SER C 164 " pdb=" C SER C 164 " pdb=" CB SER C 164 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA VAL E 106 " pdb=" N VAL E 106 " pdb=" C VAL E 106 " pdb=" CB VAL E 106 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2715 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 286 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO E 287 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO E 287 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 287 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 286 " -0.086 5.00e-02 4.00e+02 1.31e-01 2.75e+01 pdb=" N PRO A 287 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 286 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO B 287 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " -0.063 5.00e-02 4.00e+02 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 205 2.41 - 3.03: 11803 3.03 - 3.66: 26364 3.66 - 4.28: 39657 4.28 - 4.90: 62847 Nonbonded interactions: 140876 Sorted by model distance: nonbonded pdb=" OE1 GLU C 217 " pdb="MG MG C1001 " model vdw 1.788 2.170 nonbonded pdb=" O1A ADP D1000 " pdb="MG MG D1001 " model vdw 1.792 2.170 nonbonded pdb=" O5' ADP C1000 " pdb="MG MG C1001 " model vdw 1.798 2.170 nonbonded pdb=" O5' ADP E1000 " pdb="MG MG E1001 " model vdw 1.820 2.170 nonbonded pdb=" O1A ADP A1000 " pdb="MG MG A1001 " model vdw 1.850 2.170 ... (remaining 140871 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 2.020 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.840 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 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 : 0.008 0.900 17509 Z= 0.716 Angle : 0.801 14.612 23688 Z= 0.428 Chirality : 0.049 1.348 2718 Planarity : 0.007 0.136 3084 Dihedral : 14.726 176.999 6798 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.71 % Favored : 95.96 % Rotamer: Outliers : 4.93 % Allowed : 8.99 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.18), residues: 2154 helix: -0.24 (0.17), residues: 870 sheet: -0.48 (0.29), residues: 342 loop : -0.67 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 259 TYR 0.009 0.001 TYR A 105 PHE 0.010 0.001 PHE F 307 TRP 0.006 0.001 TRP C 388 HIS 0.004 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00447 (17508) covalent geometry : angle 0.80137 (23688) hydrogen bonds : bond 0.18128 ( 752) hydrogen bonds : angle 6.78565 ( 2142) Misc. bond : bond 0.89971 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 454 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8740 (tp) cc_final: 0.8494 (tt) REVERT: A 252 PHE cc_start: 0.8342 (m-10) cc_final: 0.8130 (m-10) REVERT: A 259 ARG cc_start: 0.8781 (tpp-160) cc_final: 0.8504 (mmp80) REVERT: A 397 MET cc_start: 0.7142 (mtt) cc_final: 0.6767 (tpp) REVERT: A 403 MET cc_start: 0.7843 (tmm) cc_final: 0.7400 (mmm) REVERT: B 163 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7019 (pp) REVERT: B 348 MET cc_start: 0.7628 (tmm) cc_final: 0.7272 (ppp) REVERT: B 357 GLU cc_start: 0.5927 (tm-30) cc_final: 0.5246 (mt-10) REVERT: B 374 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7844 (mmp80) REVERT: B 416 ASN cc_start: 0.9505 (t0) cc_final: 0.9293 (t0) REVERT: C 60 ARG cc_start: 0.2302 (OUTLIER) cc_final: 0.1940 (tmm160) REVERT: C 105 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5442 (p90) REVERT: C 221 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7999 (mt-10) REVERT: C 349 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5835 (pp20) REVERT: C 351 HIS cc_start: 0.6618 (m-70) cc_final: 0.6109 (t-90) REVERT: C 396 ASP cc_start: 0.7804 (m-30) cc_final: 0.7551 (p0) REVERT: D 194 LEU cc_start: 0.8698 (tp) cc_final: 0.8441 (tt) REVERT: D 221 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8037 (mt-10) REVERT: D 235 ILE cc_start: 0.7698 (mm) cc_final: 0.7253 (tp) REVERT: D 297 ASP cc_start: 0.5083 (OUTLIER) cc_final: 0.4716 (m-30) REVERT: D 349 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5967 (pp20) REVERT: D 351 HIS cc_start: 0.6355 (m-70) cc_final: 0.6017 (t-90) REVERT: D 403 MET cc_start: 0.7914 (mmm) cc_final: 0.7685 (mtm) REVERT: E 65 TYR cc_start: 0.4501 (OUTLIER) cc_final: 0.3846 (m-80) REVERT: E 349 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.4986 (pp20) REVERT: E 351 HIS cc_start: 0.6532 (m-70) cc_final: 0.5978 (t-90) REVERT: E 410 LEU cc_start: 0.7547 (mt) cc_final: 0.7293 (pp) REVERT: F 125 VAL cc_start: 0.0616 (OUTLIER) cc_final: -0.1453 (t) REVERT: F 221 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8207 (mt-10) REVERT: F 259 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8359 (mmm-85) REVERT: F 296 LEU cc_start: 0.8440 (mt) cc_final: 0.8221 (mp) REVERT: F 297 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: F 349 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.4355 (tt0) REVERT: F 351 HIS cc_start: 0.6547 (m-70) cc_final: 0.5964 (t-90) outliers start: 90 outliers final: 16 residues processed: 528 average time/residue: 0.1729 time to fit residues: 122.1611 Evaluate side-chains 267 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 240 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 388 TRP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain D residue 65 TYR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 65 TYR Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 349 GLU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 297 ASP Chi-restraints excluded: chain F residue 347 ASN Chi-restraints excluded: chain F residue 349 GLU Chi-restraints excluded: chain F residue 396 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 246 HIS B 70 GLN B 148 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 HIS C 97 GLN C 246 HIS C 281 ASN C 282 ASN D 148 GLN D 246 HIS E 148 GLN E 204 ASN E 254 HIS E 385 HIS F 129 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.124679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.099381 restraints weight = 68992.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.101777 restraints weight = 45931.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.103407 restraints weight = 35056.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.104497 restraints weight = 29245.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.104925 restraints weight = 25919.045| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17509 Z= 0.170 Angle : 0.842 10.447 23688 Z= 0.411 Chirality : 0.048 0.192 2718 Planarity : 0.007 0.142 3084 Dihedral : 11.637 145.531 2525 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.06 % Favored : 96.52 % Rotamer: Outliers : 3.51 % Allowed : 15.08 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.17), residues: 2154 helix: -0.19 (0.16), residues: 900 sheet: 0.01 (0.30), residues: 330 loop : -0.61 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 276 TYR 0.020 0.002 TYR C 98 PHE 0.020 0.002 PHE B 307 TRP 0.015 0.002 TRP E 388 HIS 0.007 0.002 HIS D 385 Details of bonding type rmsd covalent geometry : bond 0.00386 (17508) covalent geometry : angle 0.84218 (23688) hydrogen bonds : bond 0.04592 ( 752) hydrogen bonds : angle 5.54410 ( 2142) Misc. bond : bond 0.00115 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.6476 (tm-30) cc_final: 0.6272 (tm-30) REVERT: A 290 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7374 (mtt180) REVERT: A 357 GLU cc_start: 0.5749 (tm-30) cc_final: 0.5430 (mm-30) REVERT: A 397 MET cc_start: 0.7865 (mtt) cc_final: 0.7315 (tpp) REVERT: A 405 MET cc_start: 0.5847 (ttp) cc_final: 0.5608 (tmm) REVERT: B 148 GLN cc_start: 0.7203 (mm-40) cc_final: 0.5496 (mp10) REVERT: B 163 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6768 (pp) REVERT: B 221 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7565 (pt0) REVERT: B 222 VAL cc_start: 0.8631 (t) cc_final: 0.8384 (t) REVERT: B 357 GLU cc_start: 0.5857 (tm-30) cc_final: 0.5304 (mm-30) REVERT: C 105 TYR cc_start: 0.5928 (OUTLIER) cc_final: 0.5060 (p90) REVERT: C 397 MET cc_start: 0.6877 (mtt) cc_final: 0.6350 (mtm) REVERT: C 405 MET cc_start: 0.5580 (ttp) cc_final: 0.4106 (ppp) REVERT: D 194 LEU cc_start: 0.8788 (tp) cc_final: 0.8478 (tt) REVERT: D 221 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7519 (mt-10) REVERT: E 221 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: E 222 VAL cc_start: 0.8845 (t) cc_final: 0.8618 (t) REVERT: E 403 MET cc_start: 0.8348 (tmm) cc_final: 0.8101 (ppp) REVERT: F 221 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7887 (mt-10) REVERT: F 405 MET cc_start: 0.6313 (ptm) cc_final: 0.5142 (ppp) outliers start: 64 outliers final: 30 residues processed: 338 average time/residue: 0.1571 time to fit residues: 72.5005 Evaluate side-chains 236 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 202 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 103 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 198 optimal weight: 0.0050 chunk 130 optimal weight: 0.0570 overall best weight: 1.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN F 97 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.122540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.097201 restraints weight = 70764.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.099660 restraints weight = 46656.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.101305 restraints weight = 35390.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.102407 restraints weight = 29509.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.103143 restraints weight = 26133.740| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17509 Z= 0.157 Angle : 0.769 8.870 23688 Z= 0.375 Chirality : 0.045 0.206 2718 Planarity : 0.007 0.138 3084 Dihedral : 10.695 143.284 2479 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.83 % Favored : 96.80 % Rotamer: Outliers : 3.40 % Allowed : 17.65 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.17), residues: 2154 helix: 0.12 (0.16), residues: 906 sheet: -0.14 (0.30), residues: 306 loop : -0.69 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 315 TYR 0.021 0.002 TYR F 98 PHE 0.023 0.002 PHE C 419 TRP 0.014 0.001 TRP E 388 HIS 0.008 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00360 (17508) covalent geometry : angle 0.76924 (23688) hydrogen bonds : bond 0.04161 ( 752) hydrogen bonds : angle 5.26558 ( 2142) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.6631 (tm-30) cc_final: 0.6407 (tm-30) REVERT: A 273 SER cc_start: 0.8022 (OUTLIER) cc_final: 0.7627 (p) REVERT: A 359 ARG cc_start: 0.8398 (ttt180) cc_final: 0.8056 (ttt180) REVERT: A 397 MET cc_start: 0.7852 (mtt) cc_final: 0.7347 (tpp) REVERT: A 405 MET cc_start: 0.5731 (ttp) cc_final: 0.5400 (tmm) REVERT: B 222 VAL cc_start: 0.8601 (t) cc_final: 0.8397 (t) REVERT: B 359 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8326 (ttp80) REVERT: B 397 MET cc_start: 0.6850 (mtm) cc_final: 0.6130 (ptp) REVERT: B 405 MET cc_start: 0.3971 (tmm) cc_final: 0.3770 (tmm) REVERT: C 105 TYR cc_start: 0.5723 (OUTLIER) cc_final: 0.4969 (p90) REVERT: C 359 ARG cc_start: 0.8495 (ttm170) cc_final: 0.7987 (mtp85) REVERT: D 221 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7557 (mt-10) REVERT: D 397 MET cc_start: 0.7846 (mtt) cc_final: 0.7271 (mtp) REVERT: D 405 MET cc_start: 0.5615 (ttp) cc_final: 0.5256 (tmm) REVERT: F 174 ILE cc_start: 0.7041 (mp) cc_final: 0.6741 (mp) REVERT: F 221 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7972 (mt-10) REVERT: F 259 ARG cc_start: 0.8542 (tpp-160) cc_final: 0.8252 (tpp-160) REVERT: F 348 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7455 (ptm) REVERT: F 405 MET cc_start: 0.6644 (ptm) cc_final: 0.5574 (ppp) outliers start: 62 outliers final: 37 residues processed: 259 average time/residue: 0.1499 time to fit residues: 55.0383 Evaluate side-chains 216 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 9.9990 chunk 183 optimal weight: 0.0270 chunk 89 optimal weight: 0.0570 chunk 154 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 120 optimal weight: 0.0070 chunk 28 optimal weight: 4.9990 chunk 197 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 GLN ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.124079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.098569 restraints weight = 71078.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.101097 restraints weight = 46691.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.102849 restraints weight = 35394.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.103989 restraints weight = 29350.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.104744 restraints weight = 25994.563| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 17509 Z= 0.138 Angle : 0.746 9.024 23688 Z= 0.360 Chirality : 0.044 0.164 2718 Planarity : 0.007 0.133 3084 Dihedral : 10.182 137.018 2475 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.44 % Favored : 96.19 % Rotamer: Outliers : 3.23 % Allowed : 18.31 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.17), residues: 2154 helix: 0.20 (0.17), residues: 906 sheet: -0.06 (0.30), residues: 288 loop : -0.81 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 290 TYR 0.021 0.002 TYR C 98 PHE 0.015 0.002 PHE A 307 TRP 0.013 0.001 TRP E 388 HIS 0.006 0.001 HIS E 385 Details of bonding type rmsd covalent geometry : bond 0.00319 (17508) covalent geometry : angle 0.74557 (23688) hydrogen bonds : bond 0.03687 ( 752) hydrogen bonds : angle 5.09034 ( 2142) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 199 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.6572 (tm-30) cc_final: 0.6300 (tm-30) REVERT: A 290 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7353 (mtt180) REVERT: A 342 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: A 359 ARG cc_start: 0.8465 (ttt180) cc_final: 0.8142 (ttt180) REVERT: A 397 MET cc_start: 0.7787 (mtt) cc_final: 0.7341 (tpp) REVERT: A 405 MET cc_start: 0.5550 (ttp) cc_final: 0.5207 (tmm) REVERT: B 151 ASP cc_start: 0.6718 (m-30) cc_final: 0.5867 (p0) REVERT: B 222 VAL cc_start: 0.8629 (t) cc_final: 0.8420 (t) REVERT: B 359 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8372 (ttp-170) REVERT: C 105 TYR cc_start: 0.5755 (OUTLIER) cc_final: 0.5066 (p90) REVERT: C 359 ARG cc_start: 0.8545 (ttm170) cc_final: 0.8155 (mtp85) REVERT: C 397 MET cc_start: 0.6740 (mtt) cc_final: 0.6473 (mtm) REVERT: D 221 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 355 ARG cc_start: 0.4788 (ptt180) cc_final: 0.4403 (ptm160) REVERT: D 374 ARG cc_start: 0.6439 (mmp-170) cc_final: 0.6062 (mmp80) REVERT: D 405 MET cc_start: 0.5595 (ttp) cc_final: 0.5237 (tmm) REVERT: F 174 ILE cc_start: 0.6930 (mp) cc_final: 0.6614 (mp) REVERT: F 348 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7288 (ptm) REVERT: F 359 ARG cc_start: 0.8520 (ttm170) cc_final: 0.8184 (ttm170) REVERT: F 405 MET cc_start: 0.6549 (ptm) cc_final: 0.5529 (ppp) outliers start: 59 outliers final: 42 residues processed: 244 average time/residue: 0.1432 time to fit residues: 50.0750 Evaluate side-chains 223 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 166 ARG Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 61 optimal weight: 0.0020 chunk 133 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN E 81 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.124073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.098666 restraints weight = 70702.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.101125 restraints weight = 46862.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.102815 restraints weight = 35714.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.103932 restraints weight = 29804.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.104675 restraints weight = 26406.265| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.6106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17509 Z= 0.135 Angle : 0.734 9.857 23688 Z= 0.351 Chirality : 0.044 0.224 2718 Planarity : 0.007 0.126 3084 Dihedral : 9.917 130.868 2474 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.48 % Favored : 96.15 % Rotamer: Outliers : 3.67 % Allowed : 18.48 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.17), residues: 2154 helix: 0.21 (0.17), residues: 912 sheet: -0.26 (0.29), residues: 306 loop : -0.63 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 290 TYR 0.016 0.001 TYR C 98 PHE 0.012 0.001 PHE A 307 TRP 0.010 0.001 TRP E 388 HIS 0.016 0.001 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00315 (17508) covalent geometry : angle 0.73377 (23688) hydrogen bonds : bond 0.03493 ( 752) hydrogen bonds : angle 4.96361 ( 2142) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 190 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9187 (pp) cc_final: 0.8860 (mm) REVERT: A 235 ILE cc_start: 0.7926 (mm) cc_final: 0.7721 (mm) REVERT: A 290 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7306 (mtt180) REVERT: A 342 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.8195 (m-10) REVERT: A 359 ARG cc_start: 0.8501 (ttt180) cc_final: 0.8215 (ttt180) REVERT: A 397 MET cc_start: 0.7732 (mtt) cc_final: 0.7256 (tpp) REVERT: A 405 MET cc_start: 0.5488 (ttp) cc_final: 0.5146 (tmm) REVERT: B 151 ASP cc_start: 0.6772 (m-30) cc_final: 0.6088 (p0) REVERT: B 163 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6604 (pp) REVERT: B 221 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7437 (pt0) REVERT: B 222 VAL cc_start: 0.8668 (t) cc_final: 0.8441 (t) REVERT: B 405 MET cc_start: 0.3633 (tmm) cc_final: 0.3418 (tmm) REVERT: C 359 ARG cc_start: 0.8550 (ttm170) cc_final: 0.7983 (mtp85) REVERT: C 405 MET cc_start: 0.5555 (ppp) cc_final: 0.5201 (tmm) REVERT: D 221 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7616 (mt-10) REVERT: D 355 ARG cc_start: 0.4780 (ptt180) cc_final: 0.4394 (ptm160) REVERT: D 374 ARG cc_start: 0.6520 (mmp-170) cc_final: 0.5793 (mmp80) REVERT: D 403 MET cc_start: 0.7152 (ptt) cc_final: 0.6834 (ptt) REVERT: D 405 MET cc_start: 0.5442 (ttp) cc_final: 0.5152 (tmm) REVERT: F 174 ILE cc_start: 0.6952 (mp) cc_final: 0.6256 (mp) REVERT: F 348 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7414 (ptp) REVERT: F 359 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8316 (ttm170) outliers start: 67 outliers final: 46 residues processed: 241 average time/residue: 0.1508 time to fit residues: 51.4377 Evaluate side-chains 214 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 71 optimal weight: 1.9990 chunk 116 optimal weight: 0.0020 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 168 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.122742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.097373 restraints weight = 70476.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.099750 restraints weight = 47425.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.101319 restraints weight = 36450.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.102434 restraints weight = 30656.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.103155 restraints weight = 27231.666| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17509 Z= 0.139 Angle : 0.729 9.266 23688 Z= 0.349 Chirality : 0.044 0.253 2718 Planarity : 0.006 0.117 3084 Dihedral : 9.523 125.058 2470 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.39 % Favored : 96.24 % Rotamer: Outliers : 4.00 % Allowed : 18.31 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.18), residues: 2154 helix: 0.25 (0.17), residues: 912 sheet: 0.08 (0.30), residues: 288 loop : -0.67 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 276 TYR 0.014 0.001 TYR C 98 PHE 0.012 0.001 PHE A 307 TRP 0.010 0.001 TRP E 388 HIS 0.010 0.001 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00328 (17508) covalent geometry : angle 0.72950 (23688) hydrogen bonds : bond 0.03434 ( 752) hydrogen bonds : angle 4.90341 ( 2142) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 173 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.9129 (pp) cc_final: 0.8749 (mm) REVERT: A 235 ILE cc_start: 0.7949 (mm) cc_final: 0.7731 (mm) REVERT: A 342 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8231 (m-10) REVERT: A 359 ARG cc_start: 0.8436 (ttt180) cc_final: 0.8177 (ttt180) REVERT: A 397 MET cc_start: 0.7352 (mtt) cc_final: 0.7046 (tpp) REVERT: A 405 MET cc_start: 0.5721 (ttp) cc_final: 0.5401 (tmm) REVERT: B 151 ASP cc_start: 0.6618 (m-30) cc_final: 0.6002 (p0) REVERT: B 221 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7203 (pt0) REVERT: B 222 VAL cc_start: 0.8597 (t) cc_final: 0.8370 (t) REVERT: C 359 ARG cc_start: 0.8519 (ttm170) cc_final: 0.7924 (mtp85) REVERT: D 221 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7548 (mt-10) REVERT: D 342 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: D 355 ARG cc_start: 0.4863 (ptt180) cc_final: 0.4467 (ptm160) REVERT: D 403 MET cc_start: 0.7075 (ptt) cc_final: 0.6776 (ptt) REVERT: F 329 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7688 (mp0) REVERT: F 405 MET cc_start: 0.5978 (ptm) cc_final: 0.5105 (ppp) outliers start: 73 outliers final: 50 residues processed: 227 average time/residue: 0.1268 time to fit residues: 42.1910 Evaluate side-chains 213 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 119 TYR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 102 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.122873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.097400 restraints weight = 70955.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.099759 restraints weight = 47553.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.101388 restraints weight = 36534.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.102474 restraints weight = 30690.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.102970 restraints weight = 27271.073| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 17509 Z= 0.135 Angle : 0.731 9.586 23688 Z= 0.348 Chirality : 0.044 0.225 2718 Planarity : 0.006 0.108 3084 Dihedral : 9.219 125.029 2470 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.67 % Favored : 95.96 % Rotamer: Outliers : 3.56 % Allowed : 18.64 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 2154 helix: 0.33 (0.17), residues: 912 sheet: -0.33 (0.26), residues: 390 loop : -0.69 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 141 TYR 0.017 0.001 TYR D 98 PHE 0.029 0.001 PHE D 339 TRP 0.009 0.001 TRP A 388 HIS 0.008 0.001 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00319 (17508) covalent geometry : angle 0.73074 (23688) hydrogen bonds : bond 0.03316 ( 752) hydrogen bonds : angle 4.84972 ( 2142) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 175 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7718 (p) REVERT: A 342 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8295 (m-10) REVERT: A 359 ARG cc_start: 0.8379 (ttt180) cc_final: 0.7993 (ttt180) REVERT: A 397 MET cc_start: 0.7392 (mtt) cc_final: 0.7115 (tpp) REVERT: A 405 MET cc_start: 0.5642 (ttp) cc_final: 0.5359 (tmm) REVERT: B 151 ASP cc_start: 0.6587 (m-30) cc_final: 0.5979 (p0) REVERT: C 359 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8126 (mtp85) REVERT: C 397 MET cc_start: 0.6246 (mtm) cc_final: 0.6045 (mtm) REVERT: D 221 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7445 (mt-10) REVERT: D 342 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: D 355 ARG cc_start: 0.4825 (ptt180) cc_final: 0.4431 (ptm160) REVERT: D 359 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7754 (ttp-170) outliers start: 65 outliers final: 52 residues processed: 225 average time/residue: 0.1259 time to fit residues: 41.8976 Evaluate side-chains 213 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 225 PHE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 112 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 180 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.121844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.096498 restraints weight = 70798.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.098846 restraints weight = 47096.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.100482 restraints weight = 36016.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.101552 restraints weight = 30163.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.102245 restraints weight = 26826.699| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 17509 Z= 0.142 Angle : 0.746 11.349 23688 Z= 0.354 Chirality : 0.044 0.223 2718 Planarity : 0.006 0.099 3084 Dihedral : 8.914 124.087 2470 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.44 % Favored : 96.19 % Rotamer: Outliers : 3.78 % Allowed : 19.13 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.18), residues: 2154 helix: 0.25 (0.17), residues: 918 sheet: -0.46 (0.26), residues: 402 loop : -0.56 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 259 TYR 0.036 0.001 TYR A 105 PHE 0.019 0.001 PHE D 339 TRP 0.010 0.001 TRP A 388 HIS 0.009 0.001 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00334 (17508) covalent geometry : angle 0.74611 (23688) hydrogen bonds : bond 0.03410 ( 752) hydrogen bonds : angle 4.83799 ( 2142) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 161 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8197 (m-10) REVERT: A 359 ARG cc_start: 0.8408 (ttt180) cc_final: 0.7996 (ttt180) REVERT: A 405 MET cc_start: 0.5679 (ttp) cc_final: 0.5472 (tmm) REVERT: B 151 ASP cc_start: 0.6629 (m-30) cc_final: 0.5982 (p0) REVERT: C 359 ARG cc_start: 0.8578 (ttm170) cc_final: 0.8116 (mtm180) REVERT: C 397 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5927 (ptp) REVERT: C 405 MET cc_start: 0.3903 (tmm) cc_final: 0.3615 (tmm) REVERT: D 221 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7642 (mt-10) REVERT: D 342 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: F 329 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7523 (mp0) REVERT: F 359 ARG cc_start: 0.8409 (ttm170) cc_final: 0.8089 (ttt180) outliers start: 69 outliers final: 55 residues processed: 213 average time/residue: 0.1352 time to fit residues: 42.7272 Evaluate side-chains 214 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 177 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.118800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.093137 restraints weight = 70814.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.095430 restraints weight = 46988.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.096976 restraints weight = 36002.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.097967 restraints weight = 30263.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.098559 restraints weight = 27045.916| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17509 Z= 0.183 Angle : 0.784 11.131 23688 Z= 0.376 Chirality : 0.045 0.243 2718 Planarity : 0.006 0.089 3084 Dihedral : 8.944 118.181 2470 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.04 % Favored : 95.59 % Rotamer: Outliers : 3.51 % Allowed : 19.79 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2154 helix: 0.04 (0.16), residues: 912 sheet: -0.37 (0.25), residues: 438 loop : -0.41 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 276 TYR 0.029 0.001 TYR A 105 PHE 0.016 0.002 PHE D 339 TRP 0.009 0.001 TRP A 388 HIS 0.007 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00418 (17508) covalent geometry : angle 0.78407 (23688) hydrogen bonds : bond 0.03823 ( 752) hydrogen bonds : angle 5.04486 ( 2142) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 160 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8325 (m-10) REVERT: A 359 ARG cc_start: 0.8601 (ttt180) cc_final: 0.7877 (ttt180) REVERT: C 359 ARG cc_start: 0.8643 (ttm170) cc_final: 0.8394 (mtm180) REVERT: C 397 MET cc_start: 0.6522 (mtm) cc_final: 0.6127 (ptp) REVERT: C 405 MET cc_start: 0.4129 (tmm) cc_final: 0.3836 (tmm) REVERT: D 221 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7857 (mt-10) REVERT: D 342 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8166 (m-10) REVERT: D 359 ARG cc_start: 0.8389 (ttm170) cc_final: 0.7713 (ttp-170) REVERT: F 131 LEU cc_start: 0.8511 (pt) cc_final: 0.7970 (mp) REVERT: F 359 ARG cc_start: 0.8558 (ttm170) cc_final: 0.8255 (ttm170) REVERT: F 403 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7821 (ppp) outliers start: 64 outliers final: 52 residues processed: 210 average time/residue: 0.1307 time to fit residues: 40.5069 Evaluate side-chains 198 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 154 optimal weight: 0.8980 chunk 177 optimal weight: 0.4980 chunk 30 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.118529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.092936 restraints weight = 69424.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.095226 restraints weight = 46038.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.096758 restraints weight = 35281.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.097541 restraints weight = 29699.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.098352 restraints weight = 26841.852| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17509 Z= 0.174 Angle : 0.780 11.350 23688 Z= 0.373 Chirality : 0.045 0.211 2718 Planarity : 0.006 0.082 3084 Dihedral : 8.811 116.753 2470 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.22 % Favored : 95.40 % Rotamer: Outliers : 3.51 % Allowed : 20.23 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 2154 helix: 0.03 (0.16), residues: 906 sheet: -0.28 (0.27), residues: 402 loop : -0.45 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 276 TYR 0.030 0.002 TYR A 105 PHE 0.016 0.002 PHE C 239 TRP 0.009 0.001 TRP A 388 HIS 0.005 0.001 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00397 (17508) covalent geometry : angle 0.77982 (23688) hydrogen bonds : bond 0.03644 ( 752) hydrogen bonds : angle 5.04163 ( 2142) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 155 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8269 (m-10) REVERT: A 359 ARG cc_start: 0.8597 (ttt180) cc_final: 0.7888 (ttt180) REVERT: C 105 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5404 (p90) REVERT: C 359 ARG cc_start: 0.8650 (ttm170) cc_final: 0.8082 (mtm180) REVERT: D 221 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7843 (mt-10) REVERT: D 225 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8226 (m-10) REVERT: D 342 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: D 359 ARG cc_start: 0.8406 (ttm170) cc_final: 0.7642 (ttp-170) REVERT: F 131 LEU cc_start: 0.8530 (pt) cc_final: 0.7969 (mp) REVERT: F 359 ARG cc_start: 0.8531 (ttm170) cc_final: 0.8299 (ttm170) REVERT: F 403 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7817 (ppp) outliers start: 64 outliers final: 49 residues processed: 204 average time/residue: 0.1209 time to fit residues: 36.9434 Evaluate side-chains 201 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Chi-restraints excluded: chain F residue 403 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 116 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.119594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.094514 restraints weight = 70094.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.096837 restraints weight = 46582.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.098383 restraints weight = 35598.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.099397 restraints weight = 29881.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.100064 restraints weight = 26615.376| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17509 Z= 0.145 Angle : 0.766 11.560 23688 Z= 0.363 Chirality : 0.044 0.204 2718 Planarity : 0.006 0.081 3084 Dihedral : 8.622 119.511 2470 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.41 % Favored : 95.26 % Rotamer: Outliers : 3.18 % Allowed : 20.61 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.18), residues: 2154 helix: 0.12 (0.17), residues: 906 sheet: -0.26 (0.27), residues: 402 loop : -0.46 (0.23), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 259 TYR 0.029 0.001 TYR A 105 PHE 0.017 0.002 PHE F 225 TRP 0.011 0.001 TRP A 388 HIS 0.005 0.001 HIS E 81 Details of bonding type rmsd covalent geometry : bond 0.00341 (17508) covalent geometry : angle 0.76612 (23688) hydrogen bonds : bond 0.03459 ( 752) hydrogen bonds : angle 4.92482 ( 2142) Misc. bond : bond 0.00019 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.65 seconds wall clock time: 56 minutes 25.19 seconds (3385.19 seconds total)