Starting phenix.real_space_refine on Sun Jun 15 17:39:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsj_34999/06_2025/8hsj_34999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsj_34999/06_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_34999/06_2025/8hsj_34999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsj_34999/06_2025/8hsj_34999.map" model { file = "/net/cci-nas-00/data/ceres_data/8hsj_34999/06_2025/8hsj_34999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsj_34999/06_2025/8hsj_34999.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.73, per 1000 atoms: 0.68 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: 4.75 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.47 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: 7.72 Time building geometry restraints manager: 5.61 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: 0.05 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: 7.380 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 50.450 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.080 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:4.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP C 388 HIS 0.004 0.001 HIS A 351 PHE 0.010 0.001 PHE F 307 TYR 0.009 0.001 TYR A 105 ARG 0.007 0.000 ARG E 259 Details of bonding type rmsd hydrogen bonds : bond 0.18128 ( 752) hydrogen bonds : angle 6.78565 ( 2142) covalent geometry : bond 0.00447 (17508) covalent geometry : angle 0.80137 (23688) 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 : 2.125 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: 0.5564 time to fit residues: 397.2791 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 : 2.267 ------------------------------------------------------------------------------- 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 182 optimal weight: 0.0970 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 0.0370 chunk 55 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 overall best weight: 1.7460 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN C 246 HIS C 281 ASN C 282 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 HIS E 70 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN E 254 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.122355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.096764 restraints weight = 70302.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.099083 restraints weight = 46846.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.100631 restraints weight = 35933.004| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17509 Z= 0.197 Angle : 0.845 9.755 23688 Z= 0.414 Chirality : 0.048 0.236 2718 Planarity : 0.008 0.141 3084 Dihedral : 11.855 148.018 2525 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.11 % Favored : 96.47 % Rotamer: Outliers : 3.62 % Allowed : 15.79 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.18), residues: 2154 helix: -0.24 (0.16), residues: 900 sheet: -0.17 (0.29), residues: 342 loop : -0.62 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 388 HIS 0.008 0.002 HIS D 385 PHE 0.020 0.002 PHE B 307 TYR 0.026 0.002 TYR C 98 ARG 0.011 0.001 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 752) hydrogen bonds : angle 5.67712 ( 2142) covalent geometry : bond 0.00450 (17508) covalent geometry : angle 0.84465 (23688) Misc. bond : bond 0.00349 ( 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 331 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 265 time to evaluate : 2.130 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7659 (mtt180) REVERT: A 334 MET cc_start: 0.7272 (ttm) cc_final: 0.7036 (ttm) REVERT: A 357 GLU cc_start: 0.5698 (tm-30) cc_final: 0.5294 (mm-30) REVERT: A 397 MET cc_start: 0.8061 (mtt) cc_final: 0.7360 (tpp) REVERT: A 405 MET cc_start: 0.5925 (ttp) cc_final: 0.5592 (tmm) REVERT: B 163 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.6979 (pp) REVERT: B 222 VAL cc_start: 0.8647 (t) cc_final: 0.8447 (t) REVERT: C 105 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.5292 (p90) REVERT: C 355 ARG cc_start: 0.5459 (ptt180) cc_final: 0.5251 (ptm160) REVERT: C 397 MET cc_start: 0.6924 (mtt) cc_final: 0.6387 (mtm) REVERT: C 405 MET cc_start: 0.5740 (ttp) cc_final: 0.4207 (ppp) REVERT: D 221 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7568 (mt-10) REVERT: E 131 LEU cc_start: 0.8731 (mt) cc_final: 0.8491 (pp) REVERT: F 221 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7935 (mt-10) REVERT: F 351 HIS cc_start: 0.6063 (m-70) cc_final: 0.5808 (t-90) outliers start: 66 outliers final: 33 residues processed: 316 average time/residue: 0.3981 time to fit residues: 172.1958 Evaluate side-chains 237 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 C residue 105 TYR Chi-restraints excluded: chain C residue 128 VAL 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 166 ARG 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 225 PHE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 288 THR 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 288 THR Chi-restraints excluded: chain F residue 303 PHE 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 76 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 210 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.121543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.096668 restraints weight = 70169.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.099073 restraints weight = 46167.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.100715 restraints weight = 35034.542| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 17509 Z= 0.162 Angle : 0.778 8.813 23688 Z= 0.379 Chirality : 0.046 0.198 2718 Planarity : 0.007 0.137 3084 Dihedral : 10.777 139.312 2483 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.79 % Favored : 96.84 % Rotamer: Outliers : 4.00 % Allowed : 17.32 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2154 helix: -0.01 (0.16), residues: 906 sheet: 0.03 (0.31), residues: 288 loop : -0.83 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 388 HIS 0.005 0.001 HIS E 81 PHE 0.014 0.002 PHE B 307 TYR 0.024 0.002 TYR F 98 ARG 0.009 0.001 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 752) hydrogen bonds : angle 5.39553 ( 2142) covalent geometry : bond 0.00374 (17508) covalent geometry : angle 0.77772 (23688) Misc. bond : bond 0.00003 ( 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 299 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 226 time to evaluate : 2.035 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: A 132 ASP cc_start: 0.8928 (t0) cc_final: 0.8631 (p0) REVERT: A 290 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7602 (mtt180) REVERT: A 342 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7653 (m-10) REVERT: A 359 ARG cc_start: 0.8463 (ttt180) cc_final: 0.8068 (ttt180) REVERT: A 397 MET cc_start: 0.7796 (mtt) cc_final: 0.7200 (tpp) REVERT: A 405 MET cc_start: 0.5651 (ttp) cc_final: 0.5266 (tmm) REVERT: C 105 TYR cc_start: 0.5909 (OUTLIER) cc_final: 0.5194 (p90) REVERT: C 355 ARG cc_start: 0.5547 (ptt180) cc_final: 0.5323 (ptm160) REVERT: D 221 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 405 MET cc_start: 0.5715 (ttp) cc_final: 0.5395 (tmm) REVERT: E 131 LEU cc_start: 0.8562 (mt) cc_final: 0.8303 (pp) REVERT: E 403 MET cc_start: 0.8405 (tmm) cc_final: 0.8123 (ppp) REVERT: F 174 ILE cc_start: 0.7169 (mp) cc_final: 0.6885 (mp) REVERT: F 221 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7992 (mt-10) REVERT: F 348 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7390 (ptm) REVERT: F 355 ARG cc_start: 0.6330 (ptt180) cc_final: 0.5534 (ppt170) REVERT: F 405 MET cc_start: 0.6134 (ptm) cc_final: 0.5291 (ppp) outliers start: 73 outliers final: 43 residues processed: 282 average time/residue: 0.3562 time to fit residues: 141.9479 Evaluate side-chains 230 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 271 LEU 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 323 LEU Chi-restraints excluded: chain A residue 342 PHE 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 229 VAL 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 229 VAL 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 166 ARG Chi-restraints excluded: chain D residue 191 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 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 193 LEU Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 253 VAL 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 349 GLU 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 229 VAL 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 372 THR 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 192 optimal weight: 0.1980 chunk 155 optimal weight: 0.0980 chunk 215 optimal weight: 0.1980 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.125819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.101161 restraints weight = 78652.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.103515 restraints weight = 52963.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.105102 restraints weight = 41227.217| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17509 Z= 0.141 Angle : 0.743 8.810 23688 Z= 0.359 Chirality : 0.045 0.169 2718 Planarity : 0.007 0.135 3084 Dihedral : 10.177 136.641 2479 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.20 % Favored : 96.43 % Rotamer: Outliers : 3.51 % Allowed : 18.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2154 helix: 0.11 (0.16), residues: 906 sheet: -0.03 (0.31), residues: 288 loop : -0.88 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 388 HIS 0.010 0.001 HIS A 351 PHE 0.015 0.002 PHE A 307 TYR 0.023 0.002 TYR A 98 ARG 0.006 0.001 ARG B 248 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 752) hydrogen bonds : angle 5.14023 ( 2142) covalent geometry : bond 0.00326 (17508) covalent geometry : angle 0.74253 (23688) Misc. bond : bond 0.00024 ( 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 268 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 1.819 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 132 ASP cc_start: 0.9039 (t0) cc_final: 0.8831 (p0) REVERT: A 342 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8312 (m-10) REVERT: A 359 ARG cc_start: 0.8550 (ttt180) cc_final: 0.8184 (ttt180) REVERT: A 397 MET cc_start: 0.7882 (mtt) cc_final: 0.7349 (tpp) REVERT: A 405 MET cc_start: 0.5586 (ttp) cc_final: 0.5214 (tmm) REVERT: B 397 MET cc_start: 0.6535 (mtm) cc_final: 0.6131 (ptp) REVERT: C 105 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.5432 (p90) REVERT: C 355 ARG cc_start: 0.5602 (ptt180) cc_final: 0.5322 (ptm160) REVERT: C 359 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8040 (mtp85) REVERT: D 221 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7604 (mt-10) REVERT: D 329 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: D 342 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8115 (m-10) REVERT: D 403 MET cc_start: 0.7600 (tpt) cc_final: 0.7383 (mtm) REVERT: D 405 MET cc_start: 0.5448 (ttp) cc_final: 0.5227 (tmm) REVERT: E 131 LEU cc_start: 0.8272 (mt) cc_final: 0.8036 (pp) REVERT: F 174 ILE cc_start: 0.7268 (mp) cc_final: 0.6964 (mp) REVERT: F 348 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7218 (ptm) REVERT: F 351 HIS cc_start: 0.5788 (m90) cc_final: 0.5342 (t-90) REVERT: F 405 MET cc_start: 0.6264 (ptm) cc_final: 0.5304 (ppp) outliers start: 64 outliers final: 46 residues processed: 249 average time/residue: 0.3585 time to fit residues: 128.5362 Evaluate side-chains 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 176 time to evaluate : 1.963 ------------------------------------------------------------------------------- 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 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU 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 225 PHE Chi-restraints excluded: chain B residue 229 VAL 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 303 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 191 THR 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 329 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 349 GLU 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 253 VAL 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 349 GLU 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 229 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 348 MET 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 61 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 108 optimal weight: 30.0000 chunk 132 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** 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** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 HIS ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.116781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.091553 restraints weight = 72613.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.093753 restraints weight = 48260.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.095233 restraints weight = 37207.942| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.6164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17509 Z= 0.243 Angle : 0.841 8.998 23688 Z= 0.410 Chirality : 0.046 0.275 2718 Planarity : 0.008 0.130 3084 Dihedral : 10.159 129.470 2474 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.81 % Favored : 95.82 % Rotamer: Outliers : 4.50 % Allowed : 18.59 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2154 helix: -0.21 (0.16), residues: 906 sheet: -0.26 (0.28), residues: 366 loop : -0.81 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 388 HIS 0.008 0.002 HIS A 351 PHE 0.018 0.002 PHE E 362 TYR 0.012 0.001 TYR F 73 ARG 0.016 0.001 ARG D 166 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 752) hydrogen bonds : angle 5.48728 ( 2142) covalent geometry : bond 0.00536 (17508) covalent geometry : angle 0.84077 (23688) Misc. bond : bond 0.00002 ( 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 249 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 167 time to evaluate : 1.857 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: A 225 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8241 (m-10) REVERT: A 333 ARG cc_start: 0.7315 (mmm-85) cc_final: 0.7009 (mmm-85) REVERT: A 342 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8007 (m-10) REVERT: A 359 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8486 (ttt180) REVERT: A 397 MET cc_start: 0.7681 (mtt) cc_final: 0.7006 (tpp) REVERT: A 405 MET cc_start: 0.5792 (ttp) cc_final: 0.5367 (tmm) REVERT: B 104 ASP cc_start: 0.5368 (OUTLIER) cc_final: 0.5079 (p0) REVERT: B 225 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8992 (m-80) REVERT: C 105 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5565 (p90) REVERT: C 225 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8761 (m-80) REVERT: C 279 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8462 (mtm-85) REVERT: C 355 ARG cc_start: 0.5696 (ptt180) cc_final: 0.5443 (ptm160) REVERT: D 221 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7975 (mt-10) REVERT: D 403 MET cc_start: 0.7990 (tpt) cc_final: 0.7502 (mtt) REVERT: E 153 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: E 397 MET cc_start: 0.7147 (ttm) cc_final: 0.6914 (ttm) REVERT: F 134 GLU cc_start: 0.8675 (tp30) cc_final: 0.8312 (mp0) REVERT: F 225 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8720 (m-80) REVERT: F 348 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7648 (ptm) outliers start: 82 outliers final: 54 residues processed: 228 average time/residue: 0.3256 time to fit residues: 107.3157 Evaluate side-chains 213 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 225 PHE Chi-restraints excluded: chain A residue 247 ILE 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 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 104 ASP 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 325 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 71 ASP 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 279 ARG Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 153 GLN 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 253 VAL 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 349 GLU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 125 VAL 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 323 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 338 ILE 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 206 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 115 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 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** C 281 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.116714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.091789 restraints weight = 71655.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.094007 restraints weight = 47435.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.095487 restraints weight = 36476.918| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 17509 Z= 0.201 Angle : 0.791 9.905 23688 Z= 0.383 Chirality : 0.045 0.307 2718 Planarity : 0.007 0.124 3084 Dihedral : 9.780 124.327 2474 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 23.43 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.95 % Favored : 95.68 % Rotamer: Outliers : 4.66 % Allowed : 18.80 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.18), residues: 2154 helix: -0.27 (0.16), residues: 912 sheet: -0.14 (0.30), residues: 330 loop : -0.82 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 388 HIS 0.007 0.002 HIS A 351 PHE 0.016 0.002 PHE C 239 TYR 0.022 0.001 TYR B 65 ARG 0.009 0.001 ARG D 166 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 752) hydrogen bonds : angle 5.34073 ( 2142) covalent geometry : bond 0.00455 (17508) covalent geometry : angle 0.79062 (23688) Misc. bond : bond 0.00017 ( 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 248 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 163 time to evaluate : 2.012 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 225 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: A 333 ARG cc_start: 0.7290 (mmm-85) cc_final: 0.7059 (mmm-85) REVERT: A 342 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: A 359 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8464 (ttt180) REVERT: A 397 MET cc_start: 0.7830 (mtt) cc_final: 0.7233 (tpp) REVERT: A 405 MET cc_start: 0.5737 (ttp) cc_final: 0.5370 (tmm) REVERT: B 259 ARG cc_start: 0.8595 (tpp-160) cc_final: 0.8185 (tpp-160) REVERT: C 105 TYR cc_start: 0.6512 (OUTLIER) cc_final: 0.5726 (p90) REVERT: C 225 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8855 (m-80) REVERT: C 279 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8489 (mtm-85) REVERT: C 355 ARG cc_start: 0.5715 (ptt180) cc_final: 0.5457 (ptm160) REVERT: D 221 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7890 (mt-10) REVERT: D 225 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8236 (m-10) REVERT: D 329 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: D 342 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: D 403 MET cc_start: 0.7924 (tpt) cc_final: 0.7451 (mtt) REVERT: E 153 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8087 (mm-40) REVERT: E 375 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: E 382 GLU cc_start: 0.8414 (mp0) cc_final: 0.8174 (pm20) REVERT: E 397 MET cc_start: 0.7066 (ttm) cc_final: 0.6816 (ttm) REVERT: F 174 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7449 (mp) REVERT: F 225 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8848 (m-80) REVERT: F 348 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7550 (ptm) outliers start: 85 outliers final: 53 residues processed: 230 average time/residue: 0.3154 time to fit residues: 106.9839 Evaluate side-chains 214 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 147 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 221 GLU Chi-restraints excluded: chain A residue 225 PHE 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 297 ASP Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 71 ASP 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 279 ARG Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 391 ARG Chi-restraints excluded: chain D residue 106 VAL 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 329 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 153 GLN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 253 VAL 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 349 GLU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 375 GLU Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 ILE 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 323 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 338 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 82 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 8 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 82 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** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN ** F 199 ASN ** 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 = 0.4614 r_free = 0.4614 target = 0.119237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.094507 restraints weight = 70274.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.096762 restraints weight = 46608.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.098289 restraints weight = 35736.387| |-----------------------------------------------------------------------------| r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.6845 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= 0.140 Angle : 0.753 8.998 23688 Z= 0.361 Chirality : 0.045 0.237 2718 Planarity : 0.006 0.118 3084 Dihedral : 9.231 121.190 2470 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.81 % Favored : 95.82 % Rotamer: Outliers : 4.00 % Allowed : 19.46 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2154 helix: -0.04 (0.16), residues: 906 sheet: -0.02 (0.29), residues: 348 loop : -0.73 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 388 HIS 0.004 0.001 HIS A 351 PHE 0.013 0.001 PHE C 239 TYR 0.030 0.002 TYR B 98 ARG 0.007 0.001 ARG A 141 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 752) hydrogen bonds : angle 5.06231 ( 2142) covalent geometry : bond 0.00331 (17508) covalent geometry : angle 0.75323 (23688) Misc. bond : bond 0.00027 ( 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 250 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 2.007 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 333 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.7063 (mmm-85) REVERT: A 340 GLU cc_start: 0.8988 (tp30) cc_final: 0.8768 (tp30) REVERT: A 342 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: A 348 MET cc_start: 0.8075 (ppp) cc_final: 0.7742 (ptm) REVERT: A 359 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8399 (ttt180) REVERT: A 397 MET cc_start: 0.7804 (mtt) cc_final: 0.7448 (tpp) REVERT: A 405 MET cc_start: 0.5656 (ttp) cc_final: 0.5454 (tmm) REVERT: C 105 TYR cc_start: 0.6631 (OUTLIER) cc_final: 0.5614 (p90) REVERT: C 349 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: C 355 ARG cc_start: 0.5648 (ptt180) cc_final: 0.5310 (ptm160) REVERT: C 359 ARG cc_start: 0.8462 (ttm170) cc_final: 0.7868 (mtp85) REVERT: D 221 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 329 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: D 342 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: D 403 MET cc_start: 0.7698 (tpt) cc_final: 0.7313 (mtt) REVERT: F 174 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7279 (mp) REVERT: F 247 ILE cc_start: 0.9107 (pt) cc_final: 0.8770 (tp) REVERT: F 348 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7524 (ptm) REVERT: F 351 HIS cc_start: 0.5855 (m90) cc_final: 0.5258 (t-90) outliers start: 73 outliers final: 52 residues processed: 230 average time/residue: 0.3013 time to fit residues: 104.7290 Evaluate side-chains 220 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 229 VAL Chi-restraints excluded: chain A residue 271 LEU 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 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL 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 B residue 338 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 71 ASP 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 C residue 338 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 385 HIS 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 303 PHE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 407 LEU Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 192 THR 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 338 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 198 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 201 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 82 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** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.119328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.094682 restraints weight = 70310.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.096978 restraints weight = 46617.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.098512 restraints weight = 35643.974| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.7072 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= 0.139 Angle : 0.753 8.908 23688 Z= 0.360 Chirality : 0.044 0.220 2718 Planarity : 0.006 0.111 3084 Dihedral : 9.052 120.346 2470 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.27 % Favored : 95.36 % Rotamer: Outliers : 4.28 % Allowed : 19.63 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2154 helix: 0.03 (0.16), residues: 900 sheet: -0.15 (0.28), residues: 366 loop : -0.61 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 388 HIS 0.009 0.001 HIS A 351 PHE 0.012 0.001 PHE C 239 TYR 0.031 0.001 TYR B 98 ARG 0.008 0.001 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 752) hydrogen bonds : angle 4.97457 ( 2142) covalent geometry : bond 0.00327 (17508) covalent geometry : angle 0.75317 (23688) Misc. bond : bond 0.00034 ( 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 250 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 2.137 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 333 ARG cc_start: 0.7322 (mmm-85) cc_final: 0.7059 (mmm-85) REVERT: A 340 GLU cc_start: 0.8938 (tp30) cc_final: 0.8697 (tp30) REVERT: A 342 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8145 (m-10) REVERT: A 348 MET cc_start: 0.7941 (ppp) cc_final: 0.7292 (ptm) REVERT: A 359 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8387 (ttt180) REVERT: A 397 MET cc_start: 0.7676 (mtt) cc_final: 0.7451 (tpp) REVERT: C 349 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: C 355 ARG cc_start: 0.5696 (ptt180) cc_final: 0.5330 (ptm160) REVERT: C 359 ARG cc_start: 0.8465 (ttm170) cc_final: 0.7899 (mtm180) REVERT: D 221 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7745 (mt-10) REVERT: D 329 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: D 342 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8333 (m-10) REVERT: D 403 MET cc_start: 0.7533 (tpt) cc_final: 0.7166 (mtt) REVERT: F 174 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7146 (mp) REVERT: F 247 ILE cc_start: 0.9045 (pt) cc_final: 0.8728 (tp) REVERT: F 348 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7481 (ptm) REVERT: F 351 HIS cc_start: 0.5746 (m90) cc_final: 0.5193 (t-90) outliers start: 78 outliers final: 58 residues processed: 227 average time/residue: 0.3298 time to fit residues: 110.4892 Evaluate side-chains 227 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 162 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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 229 VAL Chi-restraints excluded: chain A residue 271 LEU 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 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL 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 B residue 334 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 98 TYR 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 325 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 391 ARG Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 349 GLU 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 192 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 VAL 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 98 TYR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 ILE 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 325 THR Chi-restraints excluded: chain F residue 338 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 24 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 90 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 ** C 82 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** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.119135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.094470 restraints weight = 70763.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.096776 restraints weight = 47053.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.098285 restraints weight = 36029.717| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 17509 Z= 0.139 Angle : 0.753 9.482 23688 Z= 0.359 Chirality : 0.044 0.220 2718 Planarity : 0.006 0.105 3084 Dihedral : 8.895 121.196 2470 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.18 % Favored : 95.45 % Rotamer: Outliers : 4.06 % Allowed : 20.01 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2154 helix: 0.08 (0.16), residues: 900 sheet: -0.18 (0.27), residues: 378 loop : -0.68 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 388 HIS 0.006 0.001 HIS A 351 PHE 0.012 0.001 PHE C 239 TYR 0.016 0.001 TYR C 98 ARG 0.005 0.001 ARG C 279 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 752) hydrogen bonds : angle 4.92792 ( 2142) covalent geometry : bond 0.00326 (17508) covalent geometry : angle 0.75319 (23688) Misc. bond : bond 0.00023 ( 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 241 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 167 time to evaluate : 2.320 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: A 96 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.5705 (mptt) REVERT: A 333 ARG cc_start: 0.7311 (mmm-85) cc_final: 0.7013 (mmm-85) REVERT: A 340 GLU cc_start: 0.8932 (tp30) cc_final: 0.8714 (tp30) REVERT: A 342 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8199 (m-10) REVERT: A 359 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8346 (ttt180) REVERT: A 405 MET cc_start: 0.4739 (tmm) cc_final: 0.4201 (tmm) REVERT: C 105 TYR cc_start: 0.6346 (OUTLIER) cc_final: 0.5305 (p90) REVERT: C 221 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7574 (pt0) REVERT: C 349 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6665 (tm-30) REVERT: C 355 ARG cc_start: 0.5690 (ptt180) cc_final: 0.5329 (ptm160) REVERT: C 359 ARG cc_start: 0.8480 (ttm170) cc_final: 0.7888 (mtm180) REVERT: D 132 ASP cc_start: 0.8741 (t70) cc_final: 0.8541 (t0) REVERT: D 221 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7707 (mt-10) REVERT: D 329 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: D 342 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8333 (m-10) REVERT: F 174 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7093 (mp) REVERT: F 247 ILE cc_start: 0.9021 (pt) cc_final: 0.8688 (tp) REVERT: F 348 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7309 (ptm) REVERT: F 351 HIS cc_start: 0.5725 (m90) cc_final: 0.5160 (t-90) REVERT: F 359 ARG cc_start: 0.8441 (ttm170) cc_final: 0.7966 (ttt180) outliers start: 74 outliers final: 58 residues processed: 219 average time/residue: 0.3213 time to fit residues: 104.8336 Evaluate side-chains 225 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 158 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 229 VAL 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 338 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 315 ARG 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 365 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 71 ASP 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 C residue 325 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 385 HIS Chi-restraints excluded: chain C residue 391 ARG Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 349 GLU 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 192 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 VAL 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 98 TYR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 ILE 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 325 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 MET 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 26 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 181 optimal weight: 0.0970 chunk 127 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 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** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.119426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.095412 restraints weight = 69059.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.097666 restraints weight = 45783.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.099221 restraints weight = 34913.353| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.7467 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= 0.134 Angle : 0.752 11.844 23688 Z= 0.357 Chirality : 0.044 0.208 2718 Planarity : 0.006 0.098 3084 Dihedral : 8.800 122.060 2470 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.36 % Favored : 95.26 % Rotamer: Outliers : 3.62 % Allowed : 20.56 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2154 helix: 0.08 (0.17), residues: 906 sheet: 0.21 (0.32), residues: 288 loop : -0.64 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 388 HIS 0.006 0.001 HIS A 351 PHE 0.011 0.001 PHE C 239 TYR 0.025 0.001 TYR C 98 ARG 0.009 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 752) hydrogen bonds : angle 4.89017 ( 2142) covalent geometry : bond 0.00316 (17508) covalent geometry : angle 0.75204 (23688) Misc. bond : bond 0.00025 ( 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 231 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 165 time to evaluate : 2.187 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: A 96 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.5740 (mptt) REVERT: A 333 ARG cc_start: 0.7239 (mmm-85) cc_final: 0.6939 (mmm-85) REVERT: A 359 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8357 (ttt180) REVERT: C 105 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.5309 (p90) REVERT: C 221 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7649 (pt0) REVERT: C 355 ARG cc_start: 0.5688 (ptt180) cc_final: 0.5338 (ptm160) REVERT: C 359 ARG cc_start: 0.8500 (ttm170) cc_final: 0.7836 (mtm180) REVERT: D 221 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7768 (mt-10) REVERT: D 329 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: D 342 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8346 (m-10) REVERT: E 78 GLU cc_start: 0.8153 (pt0) cc_final: 0.7748 (mm-30) REVERT: F 174 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7096 (mp) REVERT: F 247 ILE cc_start: 0.9055 (pt) cc_final: 0.8720 (tp) REVERT: F 351 HIS cc_start: 0.5862 (m90) cc_final: 0.5270 (t-90) REVERT: F 355 ARG cc_start: 0.6178 (ptt180) cc_final: 0.5823 (ptm160) outliers start: 66 outliers final: 54 residues processed: 209 average time/residue: 0.3147 time to fit residues: 98.3313 Evaluate side-chains 218 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 158 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 229 VAL 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 338 ILE Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 VAL 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 334 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 71 ASP 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 325 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 391 ARG Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 349 GLU 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 192 THR Chi-restraints excluded: chain E residue 253 VAL 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 98 TYR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 192 THR 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 338 ILE Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 53 optimal weight: 0.0170 chunk 99 optimal weight: 1.9990 overall best weight: 2.1824 ------------------------------------------------------------------------------- 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 82 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** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.116032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.091729 restraints weight = 70740.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.093856 restraints weight = 47079.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.095307 restraints weight = 36098.608| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.7712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17509 Z= 0.194 Angle : 0.804 11.203 23688 Z= 0.386 Chirality : 0.045 0.245 2718 Planarity : 0.007 0.088 3084 Dihedral : 9.012 118.223 2470 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.92 % Favored : 94.71 % Rotamer: Outliers : 3.40 % Allowed : 20.83 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2154 helix: -0.19 (0.16), residues: 906 sheet: -0.16 (0.27), residues: 378 loop : -0.73 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 388 HIS 0.014 0.002 HIS D 246 PHE 0.014 0.002 PHE C 239 TYR 0.030 0.002 TYR C 98 ARG 0.010 0.001 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 752) hydrogen bonds : angle 5.18903 ( 2142) covalent geometry : bond 0.00436 (17508) covalent geometry : angle 0.80399 (23688) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6904.49 seconds wall clock time: 121 minutes 29.27 seconds (7289.27 seconds total)