Starting phenix.real_space_refine on Sat Sep 28 00:31:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/09_2024/8hsj_34999.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/09_2024/8hsj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/09_2024/8hsj_34999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/09_2024/8hsj_34999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/09_2024/8hsj_34999.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hsj_34999/09_2024/8hsj_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.45, per 1000 atoms: 0.66 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: 4.97 Conformation dependent library (CDL) restraints added in 2.3 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: 5.34 Time building geometry restraints manager: 5.63 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: 0.00 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: 4.150 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 41.640 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.570 ------------------------------------------------------------------------------- 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 : 0.004 0.087 17508 Z= 0.297 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 *********************** 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 fitting. rotamer outliers: 90 poor density : 454 time to evaluate : 2.131 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: 0.8495 (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: 0.7401 (mmm) REVERT: B 163 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7017 (pp) REVERT: B 348 MET cc_start: 0.7628 (tmm) cc_final: 0.7273 (ppp) REVERT: B 357 GLU cc_start: 0.5927 (tm-30) cc_final: 0.5245 (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: 0.1939 (tmm160) REVERT: C 105 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.5443 (p90) REVERT: C 221 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7998 (mt-10) REVERT: C 349 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.5828 (pp20) REVERT: C 351 HIS cc_start: 0.6618 (m-70) cc_final: 0.6110 (t-90) REVERT: C 396 ASP cc_start: 0.7804 (m-30) cc_final: 0.7550 (p0) REVERT: D 194 LEU cc_start: 0.8698 (tp) cc_final: 0.8442 (tt) REVERT: D 221 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8038 (mt-10) REVERT: D 235 ILE cc_start: 0.7698 (mm) cc_final: 0.7252 (tp) REVERT: D 297 ASP cc_start: 0.5083 (OUTLIER) cc_final: 0.4715 (m-30) REVERT: D 349 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5968 (pp20) REVERT: D 351 HIS cc_start: 0.6355 (m-70) cc_final: 0.6018 (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: 0.3847 (m-80) REVERT: E 349 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.4979 (pp20) REVERT: E 351 HIS cc_start: 0.6532 (m-70) cc_final: 0.5980 (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: 0.4356 (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: 0.4380 time to fit residues: 309.3175 Evaluate side-chains 267 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17508 Z= 0.302 Angle : 0.859 10.127 23688 Z= 0.423 Chirality : 0.048 0.248 2718 Planarity : 0.008 0.142 3084 Dihedral : 11.862 147.138 2525 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.20 % Favored : 96.38 % Rotamer: Outliers : 3.67 % Allowed : 15.52 % Favored : 80.81 % 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: -0.73 (0.17), residues: 2154 helix: -0.28 (0.16), residues: 900 sheet: -0.18 (0.29), residues: 342 loop : -0.63 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 388 HIS 0.007 0.002 HIS B 351 PHE 0.021 0.002 PHE B 307 TYR 0.029 0.002 TYR C 98 ARG 0.011 0.001 ARG F 374 *********************** 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 333 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 266 time to evaluate : 2.014 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: A 109 GLN cc_start: 0.6288 (tm-30) cc_final: 0.6048 (tm-30) REVERT: A 290 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7568 (mtt180) REVERT: A 334 MET cc_start: 0.7353 (ttm) cc_final: 0.7127 (ttm) REVERT: A 357 GLU cc_start: 0.5689 (tm-30) cc_final: 0.5244 (mm-30) REVERT: A 397 MET cc_start: 0.8048 (mtt) cc_final: 0.7379 (tpp) REVERT: A 405 MET cc_start: 0.5776 (ttp) cc_final: 0.5523 (tmm) REVERT: B 163 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7144 (pp) REVERT: C 105 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5218 (p90) REVERT: C 221 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7967 (mt-10) REVERT: C 397 MET cc_start: 0.6724 (mtt) cc_final: 0.6173 (mtm) REVERT: C 405 MET cc_start: 0.5820 (ttp) cc_final: 0.4367 (ppp) REVERT: D 221 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7849 (mt-10) REVERT: D 349 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7088 (pp20) REVERT: E 131 LEU cc_start: 0.8721 (mt) cc_final: 0.8488 (pp) REVERT: E 349 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6639 (pt0) REVERT: E 351 HIS cc_start: 0.6224 (m-70) cc_final: 0.5847 (t-90) REVERT: E 403 MET cc_start: 0.8283 (tmm) cc_final: 0.7971 (ppp) REVERT: E 410 LEU cc_start: 0.7574 (mt) cc_final: 0.7327 (pp) REVERT: F 221 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8073 (mt-10) REVERT: F 259 ARG cc_start: 0.8843 (tpp-160) cc_final: 0.8580 (mmm-85) REVERT: F 351 HIS cc_start: 0.6304 (m-70) cc_final: 0.5715 (t-90) outliers start: 67 outliers final: 33 residues processed: 318 average time/residue: 0.4008 time to fit residues: 173.8540 Evaluate side-chains 242 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 2.094 ------------------------------------------------------------------------------- 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 284 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 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 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 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 349 GLU 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 109 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 196 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 282 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17508 Z= 0.235 Angle : 0.774 8.895 23688 Z= 0.378 Chirality : 0.046 0.211 2718 Planarity : 0.007 0.138 3084 Dihedral : 10.769 139.146 2489 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.37 % Allowed : 2.83 % Favored : 96.80 % Rotamer: Outliers : 3.78 % Allowed : 16.94 % Favored : 79.28 % 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: -0.61 (0.17), residues: 2154 helix: 0.02 (0.16), residues: 906 sheet: -0.17 (0.30), residues: 306 loop : -0.77 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 388 HIS 0.011 0.001 HIS A 351 PHE 0.017 0.002 PHE C 252 TYR 0.019 0.002 TYR F 98 ARG 0.009 0.001 ARG F 256 *********************** 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 294 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 225 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLN cc_start: 0.6536 (tm-30) cc_final: 0.6305 (tm-30) REVERT: A 290 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7555 (mtt180) REVERT: A 359 ARG cc_start: 0.8388 (ttt180) cc_final: 0.7998 (ttt180) REVERT: A 397 MET cc_start: 0.7936 (mtt) cc_final: 0.7406 (tpp) REVERT: A 405 MET cc_start: 0.5628 (ttp) cc_final: 0.5223 (tmm) REVERT: B 359 ARG cc_start: 0.8470 (mtp85) cc_final: 0.8258 (ttp-170) REVERT: C 105 TYR cc_start: 0.5977 (OUTLIER) cc_final: 0.5180 (p90) REVERT: C 221 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7988 (mt-10) REVERT: D 221 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7901 (mt-10) REVERT: D 405 MET cc_start: 0.5587 (ttp) cc_final: 0.5283 (tmm) REVERT: E 403 MET cc_start: 0.8332 (tmm) cc_final: 0.8115 (ppp) REVERT: E 410 LEU cc_start: 0.7762 (mt) cc_final: 0.7419 (pp) REVERT: F 221 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8160 (mt-10) REVERT: F 255 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8911 (tp30) REVERT: F 259 ARG cc_start: 0.8832 (tpp-160) cc_final: 0.8451 (tpp-160) REVERT: F 405 MET cc_start: 0.6125 (ptm) cc_final: 0.5196 (ppp) outliers start: 69 outliers final: 37 residues processed: 275 average time/residue: 0.3657 time to fit residues: 140.4281 Evaluate side-chains 222 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 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 229 VAL 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 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 253 VAL Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 396 ASP 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 193 LEU Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 253 VAL 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 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 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 194 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 208 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** ** 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 ** 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17508 Z= 0.271 Angle : 0.766 8.605 23688 Z= 0.373 Chirality : 0.045 0.161 2718 Planarity : 0.007 0.135 3084 Dihedral : 10.310 136.572 2475 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.20 % Favored : 96.43 % Rotamer: Outliers : 3.67 % Allowed : 17.98 % Favored : 78.34 % 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: 0.03 (0.16), residues: 906 sheet: 0.08 (0.31), residues: 288 loop : -0.91 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 388 HIS 0.010 0.002 HIS B 351 PHE 0.014 0.002 PHE B 307 TYR 0.030 0.002 TYR C 98 ARG 0.008 0.001 ARG D 166 *********************** 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 251 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 184 time to evaluate : 2.196 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 109 GLN cc_start: 0.6570 (tm-30) cc_final: 0.6276 (tm-30) REVERT: A 342 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8101 (m-10) REVERT: A 359 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8109 (ttt180) REVERT: A 397 MET cc_start: 0.7884 (mtt) cc_final: 0.7213 (tpp) REVERT: A 405 MET cc_start: 0.5684 (ttp) cc_final: 0.5236 (tmm) REVERT: B 359 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8255 (ttp80) REVERT: B 397 MET cc_start: 0.6520 (mtm) cc_final: 0.6213 (ptp) REVERT: C 105 TYR cc_start: 0.5957 (OUTLIER) cc_final: 0.5191 (p90) REVERT: C 221 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8072 (mt-10) REVERT: C 359 ARG cc_start: 0.8585 (ttm170) cc_final: 0.7964 (mtp85) REVERT: D 221 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8062 (mt-10) REVERT: D 405 MET cc_start: 0.5551 (ttp) cc_final: 0.5261 (tmm) REVERT: E 397 MET cc_start: 0.6644 (ttm) cc_final: 0.6370 (ttm) REVERT: F 221 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8137 (mt-10) REVERT: F 351 HIS cc_start: 0.6179 (m90) cc_final: 0.5223 (t-90) REVERT: F 405 MET cc_start: 0.6042 (ptm) cc_final: 0.5009 (ppp) outliers start: 67 outliers final: 48 residues processed: 235 average time/residue: 0.3295 time to fit residues: 112.8578 Evaluate side-chains 213 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 163 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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 378 LEU 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 B residue 338 ILE 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 349 GLU 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 396 ASP 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 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 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 259 ARG 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 372 THR Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 52 optimal weight: 0.0170 overall best weight: 1.2022 ------------------------------------------------------------------------------- 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 ** 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** ** 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** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 17508 Z= 0.228 Angle : 0.743 8.789 23688 Z= 0.356 Chirality : 0.044 0.243 2718 Planarity : 0.007 0.131 3084 Dihedral : 9.887 132.298 2475 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.30 % Favored : 96.33 % Rotamer: Outliers : 3.95 % Allowed : 18.42 % Favored : 77.63 % 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 (0.18), residues: 2154 helix: 0.05 (0.16), residues: 912 sheet: -0.11 (0.30), residues: 306 loop : -0.79 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 388 HIS 0.006 0.001 HIS F 351 PHE 0.013 0.002 PHE C 239 TYR 0.010 0.001 TYR A 98 ARG 0.007 0.001 ARG D 166 *********************** 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 fitting. rotamer outliers: 72 poor density : 177 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6916 (mmm-85) REVERT: A 342 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: A 348 MET cc_start: 0.8180 (ppp) cc_final: 0.7941 (ptm) REVERT: A 359 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8269 (ttt180) REVERT: A 397 MET cc_start: 0.7847 (mtt) cc_final: 0.7344 (tpp) REVERT: A 405 MET cc_start: 0.5602 (ttp) cc_final: 0.5207 (tmm) REVERT: B 397 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6286 (ptp) REVERT: B 405 MET cc_start: 0.3416 (tmm) cc_final: 0.3201 (tmm) REVERT: C 221 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8072 (mt-10) REVERT: D 221 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8014 (mt-10) REVERT: D 342 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: D 403 MET cc_start: 0.7816 (tpt) cc_final: 0.7441 (mtm) REVERT: E 153 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8265 (mm-40) REVERT: E 397 MET cc_start: 0.6734 (ttm) cc_final: 0.6469 (ttm) REVERT: F 221 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8201 (mt-10) REVERT: F 351 HIS cc_start: 0.6196 (m90) cc_final: 0.5620 (t-90) REVERT: F 355 ARG cc_start: 0.6459 (ptt180) cc_final: 0.5597 (ppt170) REVERT: F 405 MET cc_start: 0.6194 (ptm) cc_final: 0.5033 (ppp) outliers start: 72 outliers final: 58 residues processed: 233 average time/residue: 0.3253 time to fit residues: 110.2363 Evaluate side-chains 221 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 159 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 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 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 B residue 338 ILE Chi-restraints excluded: chain B residue 397 MET 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 349 GLU Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 342 PHE 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 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 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 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 259 ARG Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 323 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 51 optimal weight: 0.1980 chunk 208 optimal weight: 4.9990 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 HIS ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17508 Z= 0.203 Angle : 0.720 8.660 23688 Z= 0.344 Chirality : 0.044 0.240 2718 Planarity : 0.006 0.125 3084 Dihedral : 9.429 125.502 2474 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.57 % Favored : 96.05 % Rotamer: Outliers : 3.73 % Allowed : 19.24 % Favored : 77.03 % 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: -0.42 (0.18), residues: 2154 helix: 0.17 (0.17), residues: 912 sheet: 0.13 (0.31), residues: 288 loop : -0.75 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 388 HIS 0.004 0.001 HIS B 351 PHE 0.011 0.001 PHE C 239 TYR 0.009 0.001 TYR F 65 ARG 0.006 0.000 ARG F 276 *********************** 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 249 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 181 time to evaluate : 1.965 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 333 ARG cc_start: 0.7327 (mmm-85) cc_final: 0.6958 (mmm-85) REVERT: A 340 GLU cc_start: 0.8958 (tp30) cc_final: 0.8749 (tp30) REVERT: A 342 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8114 (m-10) REVERT: A 359 ARG cc_start: 0.8499 (ttt180) cc_final: 0.8123 (ttt180) REVERT: A 397 MET cc_start: 0.7860 (mtt) cc_final: 0.7502 (tpp) REVERT: A 405 MET cc_start: 0.5644 (ttp) cc_final: 0.5366 (tmm) REVERT: B 221 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7738 (pt0) REVERT: B 222 VAL cc_start: 0.8709 (t) cc_final: 0.8477 (t) REVERT: B 403 MET cc_start: 0.7590 (ppp) cc_final: 0.6820 (pmm) REVERT: C 221 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8036 (mt-10) REVERT: C 359 ARG cc_start: 0.8548 (ttm170) cc_final: 0.8054 (mtm180) REVERT: C 397 MET cc_start: 0.6131 (mtm) cc_final: 0.5851 (mtm) REVERT: D 221 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7927 (mt-10) REVERT: D 342 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: D 403 MET cc_start: 0.7819 (tpt) cc_final: 0.7504 (mtt) REVERT: E 397 MET cc_start: 0.6717 (ttm) cc_final: 0.6501 (ttm) REVERT: F 174 ILE cc_start: 0.7804 (mp) cc_final: 0.7583 (mp) REVERT: F 348 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7598 (ptm) REVERT: F 355 ARG cc_start: 0.6446 (ptt180) cc_final: 0.5550 (ppt170) REVERT: F 405 MET cc_start: 0.6018 (ptm) cc_final: 0.5328 (ppp) outliers start: 68 outliers final: 49 residues processed: 233 average time/residue: 0.3383 time to fit residues: 115.7674 Evaluate side-chains 216 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 164 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 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 192 THR Chi-restraints excluded: chain B residue 229 VAL 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 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 342 PHE Chi-restraints excluded: chain D residue 348 MET 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 229 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 372 THR 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 192 THR Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 259 ARG Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 385 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 96 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 ASN ** B 199 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 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17508 Z= 0.211 Angle : 0.724 9.101 23688 Z= 0.346 Chirality : 0.044 0.215 2718 Planarity : 0.006 0.118 3084 Dihedral : 9.132 123.608 2470 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.57 % Favored : 96.05 % Rotamer: Outliers : 4.00 % Allowed : 19.52 % Favored : 76.48 % 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: -0.33 (0.18), residues: 2154 helix: 0.19 (0.17), residues: 912 sheet: 0.11 (0.30), residues: 306 loop : -0.60 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 388 HIS 0.009 0.001 HIS A 351 PHE 0.015 0.001 PHE F 252 TYR 0.014 0.001 TYR A 98 ARG 0.023 0.001 ARG F 256 *********************** 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 243 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 170 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.7315 (mmm-85) cc_final: 0.6951 (mmm-85) REVERT: A 342 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8010 (m-10) REVERT: A 359 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8287 (ttt180) REVERT: A 397 MET cc_start: 0.7805 (mtt) cc_final: 0.7506 (tpp) REVERT: A 405 MET cc_start: 0.5637 (ttp) cc_final: 0.5363 (tmm) REVERT: B 221 GLU cc_start: 0.8486 (mt-10) cc_final: 0.7857 (pt0) REVERT: B 222 VAL cc_start: 0.8652 (t) cc_final: 0.8433 (t) REVERT: C 221 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8089 (mt-10) REVERT: C 359 ARG cc_start: 0.8584 (ttm170) cc_final: 0.8000 (mtp85) REVERT: C 397 MET cc_start: 0.6149 (mtm) cc_final: 0.5904 (ptp) REVERT: D 221 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7957 (mt-10) REVERT: D 342 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7887 (m-10) REVERT: D 403 MET cc_start: 0.7784 (tpt) cc_final: 0.7447 (mtt) REVERT: E 66 LEU cc_start: 0.7144 (pt) cc_final: 0.6894 (pt) REVERT: F 348 MET cc_start: 0.7834 (ptm) cc_final: 0.7356 (ptm) REVERT: F 405 MET cc_start: 0.6237 (ptm) cc_final: 0.5362 (ppp) outliers start: 73 outliers final: 53 residues processed: 226 average time/residue: 0.3514 time to fit residues: 117.7502 Evaluate side-chains 213 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 157 time to evaluate : 2.084 ------------------------------------------------------------------------------- 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 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 174 ILE Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 225 PHE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 342 PHE 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 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 342 PHE Chi-restraints excluded: chain D residue 365 ILE 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 229 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 372 THR 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 192 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 338 ILE 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 128 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 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** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.6872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 17508 Z= 0.221 Angle : 0.723 9.604 23688 Z= 0.346 Chirality : 0.044 0.221 2718 Planarity : 0.006 0.111 3084 Dihedral : 8.953 122.594 2470 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.81 % Favored : 95.82 % Rotamer: Outliers : 4.00 % Allowed : 19.57 % Favored : 76.43 % 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: -0.38 (0.18), residues: 2154 helix: 0.17 (0.17), residues: 912 sheet: -0.03 (0.29), residues: 324 loop : -0.62 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 388 HIS 0.007 0.001 HIS A 351 PHE 0.015 0.001 PHE F 252 TYR 0.012 0.001 TYR E 98 ARG 0.008 0.001 ARG F 256 *********************** 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 234 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 161 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8078 (m-10) REVERT: A 359 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8241 (ttt180) REVERT: A 397 MET cc_start: 0.7714 (mtt) cc_final: 0.7433 (tpp) REVERT: A 405 MET cc_start: 0.5519 (ttp) cc_final: 0.5275 (tmm) REVERT: C 359 ARG cc_start: 0.8546 (ttm170) cc_final: 0.7901 (mtp85) REVERT: C 397 MET cc_start: 0.5908 (mtm) cc_final: 0.5588 (mtm) REVERT: D 98 TYR cc_start: 0.6064 (m-80) cc_final: 0.4972 (m-80) REVERT: D 221 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 342 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7894 (m-10) REVERT: D 403 MET cc_start: 0.7778 (tpt) cc_final: 0.7377 (mtt) REVERT: E 403 MET cc_start: 0.7914 (tmm) cc_final: 0.7294 (ptp) REVERT: F 355 ARG cc_start: 0.6558 (ptt180) cc_final: 0.6282 (ptm160) REVERT: F 405 MET cc_start: 0.6110 (ptm) cc_final: 0.5171 (ppp) outliers start: 73 outliers final: 57 residues processed: 215 average time/residue: 0.3206 time to fit residues: 101.5627 Evaluate side-chains 215 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 155 time to evaluate : 2.062 ------------------------------------------------------------------------------- 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 192 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 342 PHE 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 253 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 349 GLU 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 342 PHE Chi-restraints excluded: chain D residue 365 ILE 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 221 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 315 ARG Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 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 192 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 323 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 6.9990 chunk 181 optimal weight: 0.4980 chunk 194 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 84 optimal weight: 0.0980 chunk 152 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN ** B 199 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 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 17508 Z= 0.209 Angle : 0.721 9.610 23688 Z= 0.343 Chirality : 0.044 0.210 2718 Planarity : 0.006 0.103 3084 Dihedral : 8.806 122.790 2470 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.85 % Favored : 95.78 % Rotamer: Outliers : 3.78 % Allowed : 19.57 % Favored : 76.64 % 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: -0.31 (0.18), residues: 2154 helix: 0.24 (0.17), residues: 906 sheet: -0.18 (0.26), residues: 390 loop : -0.53 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 388 HIS 0.007 0.001 HIS A 351 PHE 0.014 0.001 PHE F 252 TYR 0.015 0.001 TYR C 98 ARG 0.008 0.001 ARG B 179 *********************** 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 235 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 166 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8222 (m-10) REVERT: A 359 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8253 (ttt180) REVERT: A 397 MET cc_start: 0.7569 (mtt) cc_final: 0.7322 (tpp) REVERT: A 405 MET cc_start: 0.5562 (ttp) cc_final: 0.5318 (tmm) REVERT: B 208 ILE cc_start: 0.9056 (mt) cc_final: 0.8819 (mm) REVERT: C 121 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.6844 (p) REVERT: C 359 ARG cc_start: 0.8560 (ttm170) cc_final: 0.7958 (mtm180) REVERT: C 405 MET cc_start: 0.4102 (tmm) cc_final: 0.3825 (tmm) REVERT: D 221 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7903 (mt-10) REVERT: D 305 LYS cc_start: 0.9229 (mtpt) cc_final: 0.9010 (mtmm) REVERT: D 341 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8144 (pp20) REVERT: D 342 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: D 403 MET cc_start: 0.7641 (tpt) cc_final: 0.7299 (mtt) REVERT: F 131 LEU cc_start: 0.8425 (pt) cc_final: 0.7796 (mp) REVERT: F 329 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7582 (mp0) REVERT: F 355 ARG cc_start: 0.6580 (ptt180) cc_final: 0.6349 (ptm160) REVERT: F 405 MET cc_start: 0.6122 (ptm) cc_final: 0.5260 (ppp) outliers start: 69 outliers final: 54 residues processed: 216 average time/residue: 0.3149 time to fit residues: 100.2614 Evaluate side-chains 213 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 154 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 192 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 121 THR 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 403 MET 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 303 PHE Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 365 ILE 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 221 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE 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 192 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 323 LEU 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 205 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 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 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17508 Z= 0.267 Angle : 0.770 10.345 23688 Z= 0.369 Chirality : 0.045 0.234 2718 Planarity : 0.006 0.094 3084 Dihedral : 8.910 119.242 2470 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.64 % Favored : 94.99 % Rotamer: Outliers : 3.56 % Allowed : 20.34 % 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: -0.46 (0.18), residues: 2154 helix: 0.05 (0.16), residues: 906 sheet: -0.26 (0.27), residues: 396 loop : -0.52 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 388 HIS 0.009 0.001 HIS A 351 PHE 0.016 0.002 PHE F 252 TYR 0.022 0.001 TYR C 98 ARG 0.007 0.001 ARG B 276 ********************** 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 218 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 153 time to evaluate : 2.050 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 96 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.5768 (mptt) REVERT: A 333 ARG cc_start: 0.7210 (mmm-85) cc_final: 0.6992 (mmm-85) REVERT: A 359 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8247 (ttt180) REVERT: A 397 MET cc_start: 0.7719 (mtt) cc_final: 0.7392 (tpp) REVERT: A 405 MET cc_start: 0.5519 (ttp) cc_final: 0.5294 (tmm) REVERT: B 208 ILE cc_start: 0.9103 (mt) cc_final: 0.8856 (mm) REVERT: C 359 ARG cc_start: 0.8589 (ttm170) cc_final: 0.7901 (mtm180) REVERT: D 221 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8004 (mt-10) REVERT: D 341 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8204 (pp20) REVERT: D 342 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7567 (m-10) REVERT: D 403 MET cc_start: 0.7719 (tpt) cc_final: 0.7367 (tmm) REVERT: E 382 GLU cc_start: 0.8462 (mp0) cc_final: 0.8236 (pm20) REVERT: F 131 LEU cc_start: 0.8550 (pt) cc_final: 0.8029 (mp) REVERT: F 348 MET cc_start: 0.7950 (ptm) cc_final: 0.7560 (ptp) REVERT: F 355 ARG cc_start: 0.6528 (ptt180) cc_final: 0.6221 (ptm160) REVERT: F 405 MET cc_start: 0.6251 (ptm) cc_final: 0.6007 (ptm) outliers start: 65 outliers final: 53 residues processed: 202 average time/residue: 0.3128 time to fit residues: 93.8574 Evaluate side-chains 206 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 268 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 ILE 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 403 MET 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 297 ASP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 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 273 SER Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain E residue 325 THR Chi-restraints excluded: chain E residue 342 PHE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 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 192 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 323 LEU 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 182 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 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** E 230 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.118721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.094072 restraints weight = 71351.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.096247 restraints weight = 47990.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.097710 restraints weight = 37059.091| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 17508 Z= 0.228 Angle : 0.748 10.495 23688 Z= 0.357 Chirality : 0.045 0.216 2718 Planarity : 0.006 0.086 3084 Dihedral : 8.758 119.060 2470 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.04 % Favored : 95.59 % Rotamer: Outliers : 3.34 % Allowed : 20.34 % Favored : 76.32 % 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 (0.18), residues: 2154 helix: 0.02 (0.16), residues: 912 sheet: -0.35 (0.27), residues: 402 loop : -0.66 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 388 HIS 0.012 0.001 HIS D 246 PHE 0.014 0.002 PHE F 252 TYR 0.044 0.001 TYR C 98 ARG 0.007 0.001 ARG B 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3574.49 seconds wall clock time: 65 minutes 2.70 seconds (3902.70 seconds total)