Starting phenix.real_space_refine on Thu Mar 5 23:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r8b_4754/03_2026/6r8b_4754_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r8b_4754/03_2026/6r8b_4754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r8b_4754/03_2026/6r8b_4754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r8b_4754/03_2026/6r8b_4754.map" model { file = "/net/cci-nas-00/data/ceres_data/6r8b_4754/03_2026/6r8b_4754_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r8b_4754/03_2026/6r8b_4754_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.156 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 84 5.16 5 C 8328 2.51 5 N 2340 2.21 5 O 2504 1.98 5 H 12788 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26052 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 6493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6493 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 400} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'FBP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.12, per 1000 atoms: 0.16 Number of scatterers: 26052 At special positions: 0 Unit cell: (105.747, 103.653, 101.559, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 8 15.00 O 2504 8.00 N 2340 7.00 C 8328 6.00 H 12788 1.00 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=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 724.7 milliseconds 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 28.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 41 through 44 Processing helix chain 'D' and resid 53 through 64 removed outlier: 3.809A pdb=" N ALA D 57 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 88 Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 116 through 121 Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 148 through 160 removed outlier: 3.669A pdb=" N MET D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 160 " --> pdb=" O HIS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.571A pdb=" N PHE D 178 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 233 removed outlier: 3.947A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 279 through 289 Processing helix chain 'D' and resid 399 through 407 Processing helix chain 'D' and resid 418 through 425 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 53 through 64 removed outlier: 3.809A pdb=" N ALA B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 88 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.669A pdb=" N MET B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 160 " --> pdb=" O HIS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.571A pdb=" N PHE B 178 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 removed outlier: 3.947A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 279 through 289 Processing helix chain 'B' and resid 399 through 407 Processing helix chain 'B' and resid 418 through 425 Processing helix chain 'A' and resid 16 through 18 No H-bonds generated for 'chain 'A' and resid 16 through 18' Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.809A pdb=" N ALA A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.669A pdb=" N MET A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.571A pdb=" N PHE A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 removed outlier: 3.947A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 418 through 425 Processing helix chain 'C' and resid 16 through 18 No H-bonds generated for 'chain 'C' and resid 16 through 18' Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.809A pdb=" N ALA C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 88 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 124 through 130 Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.670A pdb=" N MET C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 160 " --> pdb=" O HIS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.571A pdb=" N PHE C 178 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 removed outlier: 3.947A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 252 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 279 through 289 Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 418 through 425 Processing sheet with id=AA1, first strand: chain 'D' and resid 98 through 103 removed outlier: 5.061A pdb=" N ARG D 68 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLY D 214 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA D 166 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE D 215 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR D 164 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS D 163 " --> pdb=" O TYR D 255 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS D 257 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 165 " --> pdb=" O HIS D 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 46 through 47 removed outlier: 3.512A pdb=" N PHE D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AA4, first strand: chain 'D' and resid 180 through 183 removed outlier: 6.936A pdb=" N VAL D 180 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE D 192 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA D 182 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 389 through 390 removed outlier: 6.368A pdb=" N TRP D 372 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG D 355 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 339 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 333 " --> pdb=" O LEU C 350 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 349 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL C 346 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL C 366 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET C 328 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET D 328 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL D 346 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL D 366 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL D 349 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 333 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 339 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG C 355 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP C 372 " --> pdb=" O ILE C 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.540A pdb=" N TYR D 408 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N VAL D 415 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG D 381 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL D 417 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 383 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ILE D 362 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N CYS D 382 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER D 364 " --> pdb=" O CYS D 382 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE D 384 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 366 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL D 346 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL D 366 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET D 328 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET C 328 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL C 346 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL C 366 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ILE C 362 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N CYS C 382 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N SER C 364 " --> pdb=" O CYS C 382 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE C 384 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 366 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N VAL C 415 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG C 381 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL C 417 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 383 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR C 408 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 103 removed outlier: 5.061A pdb=" N ARG B 68 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLY B 214 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 166 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 215 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR B 164 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS B 163 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N HIS B 257 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B 165 " --> pdb=" O HIS B 257 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47 removed outlier: 3.513A pdb=" N PHE B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AB1, first strand: chain 'B' and resid 180 through 183 removed outlier: 6.936A pdb=" N VAL B 180 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE B 192 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 182 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.368A pdb=" N TRP B 372 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 355 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 339 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 333 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 349 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL A 346 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 366 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET A 328 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET B 328 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N VAL B 346 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL B 366 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 349 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 333 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL A 339 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG A 355 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 372 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.540A pdb=" N TYR B 408 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 10.289A pdb=" N VAL B 415 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG B 381 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL B 417 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 383 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ILE B 362 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N CYS B 382 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER B 364 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE B 384 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 366 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N VAL B 346 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL B 366 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET B 328 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N MET A 328 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N VAL A 346 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 366 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N ILE A 362 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N CYS A 382 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N SER A 364 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ILE A 384 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL A 366 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N VAL A 415 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG A 381 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL A 417 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 383 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 408 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 98 through 103 removed outlier: 5.061A pdb=" N ARG A 68 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLY A 214 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA A 166 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 215 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 164 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS A 163 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS A 257 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 165 " --> pdb=" O HIS A 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.512A pdb=" N PHE A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 144 through 145 Processing sheet with id=AB7, first strand: chain 'A' and resid 180 through 183 removed outlier: 6.937A pdb=" N VAL A 180 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE A 192 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 182 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 98 through 103 removed outlier: 5.061A pdb=" N ARG C 68 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY C 214 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA C 166 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 215 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR C 164 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS C 163 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N HIS C 257 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL C 165 " --> pdb=" O HIS C 257 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 46 through 47 removed outlier: 3.512A pdb=" N PHE C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AC2, first strand: chain 'C' and resid 180 through 183 removed outlier: 6.936A pdb=" N VAL C 180 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE C 192 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 182 " --> pdb=" O ILE C 190 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 12752 1.04 - 1.23: 877 1.23 - 1.43: 4859 1.43 - 1.63: 7704 1.63 - 1.83: 132 Bond restraints: 26324 Sorted by residual: bond pdb=" C5 FBP A 501 " pdb=" O5 FBP A 501 " ideal model delta sigma weight residual 1.608 1.430 0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C5 FBP D 501 " pdb=" O5 FBP D 501 " ideal model delta sigma weight residual 1.608 1.430 0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" C5 FBP C 501 " pdb=" O5 FBP C 501 " ideal model delta sigma weight residual 1.608 1.431 0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C5 FBP B 501 " pdb=" O5 FBP B 501 " ideal model delta sigma weight residual 1.608 1.431 0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C4 FBP C 501 " pdb=" C5 FBP C 501 " ideal model delta sigma weight residual 1.346 1.512 -0.166 2.00e-02 2.50e+03 6.85e+01 ... (remaining 26319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 43024 2.45 - 4.90: 4153 4.90 - 7.35: 235 7.35 - 9.80: 24 9.80 - 12.25: 8 Bond angle restraints: 47444 Sorted by residual: angle pdb=" N ARG B 115 " pdb=" CA ARG B 115 " pdb=" C ARG B 115 " ideal model delta sigma weight residual 111.56 101.33 10.23 1.43e+00 4.89e-01 5.12e+01 angle pdb=" N ARG C 115 " pdb=" CA ARG C 115 " pdb=" C ARG C 115 " ideal model delta sigma weight residual 111.56 101.35 10.21 1.43e+00 4.89e-01 5.10e+01 angle pdb=" N ARG D 115 " pdb=" CA ARG D 115 " pdb=" C ARG D 115 " ideal model delta sigma weight residual 111.56 101.35 10.21 1.43e+00 4.89e-01 5.10e+01 angle pdb=" N ARG A 115 " pdb=" CA ARG A 115 " pdb=" C ARG A 115 " ideal model delta sigma weight residual 111.56 101.35 10.21 1.43e+00 4.89e-01 5.09e+01 angle pdb=" N SER B 89 " pdb=" CA SER B 89 " pdb=" C SER B 89 " ideal model delta sigma weight residual 110.65 102.99 7.66 1.26e+00 6.30e-01 3.70e+01 ... (remaining 47439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 11254 17.23 - 34.45: 808 34.45 - 51.68: 324 51.68 - 68.91: 130 68.91 - 86.14: 16 Dihedral angle restraints: 12532 sinusoidal: 6880 harmonic: 5652 Sorted by residual: dihedral pdb=" C PHE A 91 " pdb=" N PHE A 91 " pdb=" CA PHE A 91 " pdb=" CB PHE A 91 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" CA GLY B 342 " pdb=" C GLY B 342 " pdb=" N SER B 343 " pdb=" CA SER B 343 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLY A 342 " pdb=" C GLY A 342 " pdb=" N SER A 343 " pdb=" CA SER A 343 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 12529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1334 0.062 - 0.123: 503 0.123 - 0.185: 143 0.185 - 0.246: 36 0.246 - 0.308: 12 Chirality restraints: 2028 Sorted by residual: chirality pdb=" CA HIS A 238 " pdb=" N HIS A 238 " pdb=" C HIS A 238 " pdb=" CB HIS A 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS C 238 " pdb=" N HIS C 238 " pdb=" C HIS C 238 " pdb=" CB HIS C 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS B 238 " pdb=" N HIS B 238 " pdb=" C HIS B 238 " pdb=" CB HIS B 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2025 not shown) Planarity restraints: 3992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 15 " 0.101 2.00e-02 2.50e+03 1.07e-01 1.73e+02 pdb=" CD GLN B 15 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN B 15 " -0.096 2.00e-02 2.50e+03 pdb=" NE2 GLN B 15 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 15 " -0.156 2.00e-02 2.50e+03 pdb="HE22 GLN B 15 " 0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 15 " -0.101 2.00e-02 2.50e+03 1.07e-01 1.73e+02 pdb=" CD GLN D 15 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN D 15 " 0.096 2.00e-02 2.50e+03 pdb=" NE2 GLN D 15 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 15 " 0.156 2.00e-02 2.50e+03 pdb="HE22 GLN D 15 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 15 " -0.101 2.00e-02 2.50e+03 1.07e-01 1.73e+02 pdb=" CD GLN C 15 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN C 15 " 0.096 2.00e-02 2.50e+03 pdb=" NE2 GLN C 15 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN C 15 " 0.155 2.00e-02 2.50e+03 pdb="HE22 GLN C 15 " -0.159 2.00e-02 2.50e+03 ... (remaining 3989 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 3081 2.26 - 2.84: 58252 2.84 - 3.43: 68563 3.43 - 4.01: 97758 4.01 - 4.60: 148619 Nonbonded interactions: 376273 Sorted by model distance: nonbonded pdb="HD21 ASN C 92 " pdb=" HB2 MET C 95 " model vdw 1.671 2.270 nonbonded pdb="HD21 ASN D 92 " pdb=" HB2 MET D 95 " model vdw 1.671 2.270 nonbonded pdb="HD21 ASN B 92 " pdb=" HB2 MET B 95 " model vdw 1.672 2.270 nonbonded pdb="HD21 ASN A 92 " pdb=" HB2 MET A 95 " model vdw 1.672 2.270 nonbonded pdb=" HZ1 LYS A 146 " pdb=" O ASP A 298 " model vdw 1.723 2.450 ... (remaining 376268 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: 0.04 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'B' selection = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.150 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.940 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 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 : 0.012 0.178 13536 Z= 0.687 Angle : 1.343 12.252 18364 Z= 0.848 Chirality : 0.073 0.308 2028 Planarity : 0.009 0.061 2400 Dihedral : 15.727 86.136 5140 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.05 % Favored : 95.71 % Rotamer: Outliers : 3.12 % Allowed : 5.95 % Favored : 90.93 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.16), residues: 1680 helix: -2.50 (0.19), residues: 468 sheet: -2.55 (0.31), residues: 164 loop : -2.05 (0.15), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 353 TYR 0.023 0.004 TYR B 131 PHE 0.026 0.004 PHE A 240 TRP 0.028 0.007 TRP D 284 HIS 0.012 0.004 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.01222 (13536) covalent geometry : angle 1.34312 (18364) hydrogen bonds : bond 0.22140 ( 392) hydrogen bonds : angle 7.97625 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 322 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 0.648 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: D 39 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7731 (tppp) REVERT: D 93 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7083 (mp0) REVERT: D 94 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6337 (pm20) REVERT: D 117 THR cc_start: 0.8099 (m) cc_final: 0.7805 (p) REVERT: D 134 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7077 (mt-10) REVERT: D 148 ASP cc_start: 0.6526 (t0) cc_final: 0.6225 (t0) REVERT: D 198 ASN cc_start: 0.7922 (t0) cc_final: 0.7532 (p0) REVERT: D 229 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7350 (mp0) REVERT: D 289 ASP cc_start: 0.6719 (t70) cc_final: 0.6140 (t0) REVERT: D 385 ASP cc_start: 0.7947 (t0) cc_final: 0.7724 (t0) REVERT: D 399 ASN cc_start: 0.6323 (t0) cc_final: 0.5760 (t0) REVERT: D 423 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6061 (mtt90) REVERT: B 93 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7064 (mp0) REVERT: B 94 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6233 (pm20) REVERT: B 117 THR cc_start: 0.8247 (m) cc_final: 0.7961 (p) REVERT: B 134 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7138 (tt0) REVERT: B 145 TYR cc_start: 0.7541 (p90) cc_final: 0.7271 (p90) REVERT: B 148 ASP cc_start: 0.6488 (t0) cc_final: 0.6157 (t0) REVERT: B 178 PHE cc_start: 0.5073 (m-80) cc_final: 0.4813 (m-80) REVERT: B 198 ASN cc_start: 0.7944 (t0) cc_final: 0.7314 (p0) REVERT: B 229 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7368 (mp0) REVERT: B 289 ASP cc_start: 0.6954 (t70) cc_final: 0.6331 (t0) REVERT: B 303 ASN cc_start: 0.8003 (m-40) cc_final: 0.7773 (m-40) REVERT: B 423 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6165 (mtt90) REVERT: A 39 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7731 (tppp) REVERT: A 93 GLU cc_start: 0.7483 (tm-30) cc_final: 0.6944 (mp0) REVERT: A 94 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: A 117 THR cc_start: 0.8151 (m) cc_final: 0.7836 (p) REVERT: A 134 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7188 (mt-10) REVERT: A 148 ASP cc_start: 0.6472 (t0) cc_final: 0.6145 (t0) REVERT: A 198 ASN cc_start: 0.7929 (t0) cc_final: 0.7486 (p0) REVERT: A 229 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7445 (mp0) REVERT: A 289 ASP cc_start: 0.6866 (t70) cc_final: 0.6246 (t0) REVERT: A 385 ASP cc_start: 0.7973 (t0) cc_final: 0.7737 (t0) REVERT: A 399 ASN cc_start: 0.6315 (t0) cc_final: 0.5763 (t0) REVERT: A 423 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6075 (mtt90) REVERT: C 117 THR cc_start: 0.8133 (m) cc_final: 0.7831 (p) REVERT: C 134 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7041 (mt-10) REVERT: C 148 ASP cc_start: 0.6492 (t0) cc_final: 0.6194 (t0) REVERT: C 178 PHE cc_start: 0.5060 (m-80) cc_final: 0.4824 (m-80) REVERT: C 221 ASP cc_start: 0.7783 (m-30) cc_final: 0.7240 (p0) REVERT: C 229 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7283 (mp0) REVERT: C 289 ASP cc_start: 0.6958 (t70) cc_final: 0.6361 (t0) REVERT: C 303 ASN cc_start: 0.8006 (m-40) cc_final: 0.7800 (m-40) REVERT: C 423 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6035 (mtt90) outliers start: 44 outliers final: 20 residues processed: 306 average time/residue: 0.3573 time to fit residues: 144.4784 Evaluate side-chains 250 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 107 ARG Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 423 ARG Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 423 ARG Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 423 ARG Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 423 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN D 85 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 ASN B 82 GLN ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS A 82 GLN A 85 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 326 HIS C 82 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.163484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125083 restraints weight = 38358.834| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.61 r_work: 0.3404 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13536 Z= 0.102 Angle : 0.527 4.710 18364 Z= 0.273 Chirality : 0.045 0.154 2028 Planarity : 0.005 0.040 2400 Dihedral : 8.203 46.242 2085 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.85 % Allowed : 9.63 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.18), residues: 1680 helix: -0.80 (0.23), residues: 460 sheet: -2.29 (0.31), residues: 160 loop : -1.44 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 353 TYR 0.009 0.001 TYR D 145 PHE 0.008 0.001 PHE A 98 TRP 0.009 0.001 TRP D 284 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00225 (13536) covalent geometry : angle 0.52661 (18364) hydrogen bonds : bond 0.03763 ( 392) hydrogen bonds : angle 5.06840 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 219 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 39 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8365 (tppp) REVERT: D 134 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7858 (mt-10) REVERT: D 198 ASN cc_start: 0.8005 (t0) cc_final: 0.7672 (p0) REVERT: D 276 ASP cc_start: 0.7889 (t70) cc_final: 0.7573 (p0) REVERT: D 289 ASP cc_start: 0.8406 (t70) cc_final: 0.7969 (t0) REVERT: B 289 ASP cc_start: 0.8441 (t70) cc_final: 0.8011 (t0) REVERT: B 303 ASN cc_start: 0.8329 (m-40) cc_final: 0.8120 (m-40) REVERT: A 39 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8385 (tppp) REVERT: A 198 ASN cc_start: 0.7990 (t0) cc_final: 0.7625 (p0) REVERT: A 276 ASP cc_start: 0.7876 (t70) cc_final: 0.7573 (p0) REVERT: A 289 ASP cc_start: 0.8409 (t70) cc_final: 0.7968 (t0) REVERT: C 39 LYS cc_start: 0.8623 (tppt) cc_final: 0.8144 (mmtp) REVERT: C 134 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7884 (mt-10) REVERT: C 168 MET cc_start: 0.7154 (ttt) cc_final: 0.6951 (ttm) REVERT: C 178 PHE cc_start: 0.5737 (m-80) cc_final: 0.5474 (m-80) REVERT: C 289 ASP cc_start: 0.8429 (t70) cc_final: 0.8006 (t0) outliers start: 12 outliers final: 11 residues processed: 226 average time/residue: 0.3180 time to fit residues: 97.7604 Evaluate side-chains 200 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 326 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 103 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121643 restraints weight = 38556.309| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.58 r_work: 0.3360 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13536 Z= 0.121 Angle : 0.500 4.766 18364 Z= 0.258 Chirality : 0.044 0.146 2028 Planarity : 0.005 0.039 2400 Dihedral : 6.290 43.972 2012 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.63 % Allowed : 8.36 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.18), residues: 1680 helix: -0.24 (0.24), residues: 460 sheet: -2.04 (0.34), residues: 160 loop : -1.19 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 353 TYR 0.006 0.001 TYR D 283 PHE 0.006 0.001 PHE D 98 TRP 0.008 0.001 TRP A 284 HIS 0.009 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00287 (13536) covalent geometry : angle 0.50044 (18364) hydrogen bonds : bond 0.03330 ( 392) hydrogen bonds : angle 4.83589 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.434 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: D 39 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8233 (tppp) REVERT: D 198 ASN cc_start: 0.8023 (t0) cc_final: 0.7663 (p0) REVERT: D 276 ASP cc_start: 0.7864 (t70) cc_final: 0.7522 (p0) REVERT: D 289 ASP cc_start: 0.8506 (t70) cc_final: 0.8104 (t0) REVERT: B 289 ASP cc_start: 0.8545 (t70) cc_final: 0.8139 (t0) REVERT: A 39 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8242 (tppp) REVERT: A 198 ASN cc_start: 0.7975 (t0) cc_final: 0.7599 (p0) REVERT: A 276 ASP cc_start: 0.7873 (t70) cc_final: 0.7578 (p0) REVERT: A 289 ASP cc_start: 0.8528 (t70) cc_final: 0.8141 (t0) REVERT: A 328 MET cc_start: 0.7924 (mtm) cc_final: 0.7627 (mtp) REVERT: C 39 LYS cc_start: 0.8597 (tppt) cc_final: 0.8147 (mmtp) REVERT: C 289 ASP cc_start: 0.8500 (t70) cc_final: 0.8093 (t0) outliers start: 23 outliers final: 20 residues processed: 205 average time/residue: 0.3356 time to fit residues: 92.1197 Evaluate side-chains 192 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 310 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 161 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS A 326 HIS ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118803 restraints weight = 38251.707| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.47 r_work: 0.3293 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13536 Z= 0.189 Angle : 0.529 5.090 18364 Z= 0.275 Chirality : 0.045 0.151 2028 Planarity : 0.005 0.048 2400 Dihedral : 6.214 43.198 2012 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.91 % Allowed : 9.35 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.19), residues: 1680 helix: 0.11 (0.25), residues: 456 sheet: -1.60 (0.39), residues: 152 loop : -1.15 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 353 TYR 0.007 0.001 TYR B 283 PHE 0.010 0.001 PHE C 259 TRP 0.010 0.001 TRP B 284 HIS 0.006 0.002 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00456 (13536) covalent geometry : angle 0.52914 (18364) hydrogen bonds : bond 0.03249 ( 392) hydrogen bonds : angle 4.86520 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.605 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: D 39 LYS cc_start: 0.8637 (mmtp) cc_final: 0.8217 (mmtp) REVERT: D 198 ASN cc_start: 0.8014 (t0) cc_final: 0.7658 (p0) REVERT: D 289 ASP cc_start: 0.8610 (t70) cc_final: 0.8289 (t0) REVERT: B 39 LYS cc_start: 0.8697 (tppt) cc_final: 0.8178 (mmtp) REVERT: B 289 ASP cc_start: 0.8598 (t70) cc_final: 0.8206 (t0) REVERT: B 421 MET cc_start: 0.8812 (mtt) cc_final: 0.8601 (mtt) REVERT: A 39 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8202 (mmtp) REVERT: A 198 ASN cc_start: 0.8052 (t0) cc_final: 0.7631 (p0) REVERT: A 276 ASP cc_start: 0.7958 (t70) cc_final: 0.7617 (p0) REVERT: A 289 ASP cc_start: 0.8578 (t70) cc_final: 0.8176 (t0) REVERT: C 39 LYS cc_start: 0.8687 (tppt) cc_final: 0.8180 (mmtp) REVERT: C 289 ASP cc_start: 0.8597 (t70) cc_final: 0.8218 (t0) outliers start: 27 outliers final: 24 residues processed: 208 average time/residue: 0.3380 time to fit residues: 95.0771 Evaluate side-chains 199 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 326 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 26 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118985 restraints weight = 37913.601| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.57 r_work: 0.3298 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13536 Z= 0.100 Angle : 0.491 5.597 18364 Z= 0.251 Chirality : 0.044 0.148 2028 Planarity : 0.005 0.050 2400 Dihedral : 5.885 43.871 2012 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 10.48 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.19), residues: 1680 helix: 0.44 (0.25), residues: 460 sheet: -1.56 (0.40), residues: 152 loop : -1.05 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 353 TYR 0.007 0.001 TYR D 145 PHE 0.009 0.001 PHE A 218 TRP 0.007 0.001 TRP A 284 HIS 0.008 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00229 (13536) covalent geometry : angle 0.49104 (18364) hydrogen bonds : bond 0.02880 ( 392) hydrogen bonds : angle 4.61128 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.722 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: D 39 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8131 (mmtp) REVERT: D 198 ASN cc_start: 0.8014 (t0) cc_final: 0.7658 (p0) REVERT: D 289 ASP cc_start: 0.8575 (t70) cc_final: 0.8262 (t0) REVERT: D 340 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8174 (mt) REVERT: D 421 MET cc_start: 0.8869 (mtt) cc_final: 0.8573 (mtt) REVERT: B 39 LYS cc_start: 0.8705 (tppt) cc_final: 0.8204 (mmtp) REVERT: B 289 ASP cc_start: 0.8555 (t70) cc_final: 0.8237 (t0) REVERT: B 340 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 353 ARG cc_start: 0.8990 (mtt-85) cc_final: 0.8761 (mtt-85) REVERT: B 421 MET cc_start: 0.8801 (mtt) cc_final: 0.8378 (mtt) REVERT: A 39 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8198 (mmtp) REVERT: A 198 ASN cc_start: 0.8042 (t0) cc_final: 0.7613 (p0) REVERT: A 276 ASP cc_start: 0.7955 (t70) cc_final: 0.7610 (p0) REVERT: A 289 ASP cc_start: 0.8554 (t70) cc_final: 0.8239 (t0) REVERT: A 340 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8195 (mt) REVERT: C 39 LYS cc_start: 0.8685 (tppt) cc_final: 0.8219 (mmtp) REVERT: C 289 ASP cc_start: 0.8557 (t70) cc_final: 0.8239 (t0) REVERT: C 340 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8215 (mt) outliers start: 29 outliers final: 21 residues processed: 208 average time/residue: 0.3386 time to fit residues: 94.8528 Evaluate side-chains 196 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 340 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 0.0870 chunk 148 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 137 optimal weight: 0.0870 chunk 120 optimal weight: 0.7980 overall best weight: 0.9938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN A 326 HIS ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN C 326 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.160362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122156 restraints weight = 38004.355| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.45 r_work: 0.3334 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13536 Z= 0.106 Angle : 0.483 4.627 18364 Z= 0.245 Chirality : 0.044 0.145 2028 Planarity : 0.004 0.038 2400 Dihedral : 5.624 44.416 2008 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.76 % Allowed : 10.06 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.19), residues: 1680 helix: 0.76 (0.25), residues: 460 sheet: -1.63 (0.41), residues: 156 loop : -1.00 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 353 TYR 0.006 0.001 TYR C 145 PHE 0.007 0.001 PHE B 259 TRP 0.007 0.001 TRP B 284 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00251 (13536) covalent geometry : angle 0.48250 (18364) hydrogen bonds : bond 0.02759 ( 392) hydrogen bonds : angle 4.51623 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.720 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: D 39 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8183 (mmtp) REVERT: D 69 MET cc_start: 0.9023 (mtm) cc_final: 0.8556 (mtt) REVERT: D 198 ASN cc_start: 0.8052 (t0) cc_final: 0.7683 (p0) REVERT: D 289 ASP cc_start: 0.8540 (t70) cc_final: 0.8220 (t0) REVERT: D 340 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B 39 LYS cc_start: 0.8727 (tppt) cc_final: 0.8281 (mmtp) REVERT: B 289 ASP cc_start: 0.8522 (t70) cc_final: 0.8205 (t0) REVERT: B 340 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8218 (mt) REVERT: B 353 ARG cc_start: 0.9042 (mtt-85) cc_final: 0.8820 (mtt-85) REVERT: B 421 MET cc_start: 0.8819 (mtt) cc_final: 0.8400 (mtt) REVERT: A 14 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8181 (ttp80) REVERT: A 39 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8158 (mmtp) REVERT: A 69 MET cc_start: 0.9023 (mtm) cc_final: 0.8579 (mtt) REVERT: A 191 GLU cc_start: 0.8118 (tp30) cc_final: 0.7908 (pt0) REVERT: A 198 ASN cc_start: 0.8056 (t0) cc_final: 0.7633 (p0) REVERT: A 271 GLU cc_start: 0.8288 (tt0) cc_final: 0.8073 (tp30) REVERT: A 289 ASP cc_start: 0.8527 (t70) cc_final: 0.8137 (t0) REVERT: A 340 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 421 MET cc_start: 0.8850 (mtt) cc_final: 0.8579 (mtt) REVERT: C 39 LYS cc_start: 0.8694 (tppt) cc_final: 0.8266 (mmtp) REVERT: C 69 MET cc_start: 0.8989 (mtm) cc_final: 0.8669 (mtt) REVERT: C 289 ASP cc_start: 0.8524 (t70) cc_final: 0.8133 (t0) REVERT: C 340 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8184 (mt) outliers start: 39 outliers final: 29 residues processed: 211 average time/residue: 0.3444 time to fit residues: 97.6787 Evaluate side-chains 199 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 126 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN C 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.158111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119463 restraints weight = 38202.733| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.47 r_work: 0.3287 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13536 Z= 0.160 Angle : 0.500 4.611 18364 Z= 0.257 Chirality : 0.045 0.147 2028 Planarity : 0.004 0.039 2400 Dihedral : 5.677 44.700 2008 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.62 % Allowed : 10.69 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.19), residues: 1680 helix: 0.75 (0.26), residues: 460 sheet: -1.60 (0.41), residues: 156 loop : -1.03 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 353 TYR 0.007 0.001 TYR C 283 PHE 0.008 0.001 PHE A 218 TRP 0.008 0.001 TRP B 284 HIS 0.008 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00385 (13536) covalent geometry : angle 0.50017 (18364) hydrogen bonds : bond 0.02914 ( 392) hydrogen bonds : angle 4.61081 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.637 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: D 39 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8200 (mmtp) REVERT: D 198 ASN cc_start: 0.8066 (t0) cc_final: 0.7662 (p0) REVERT: D 289 ASP cc_start: 0.8544 (t70) cc_final: 0.8164 (t0) REVERT: D 303 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7983 (t0) REVERT: B 39 LYS cc_start: 0.8739 (tppt) cc_final: 0.8316 (mmtp) REVERT: B 289 ASP cc_start: 0.8534 (t70) cc_final: 0.8156 (t0) REVERT: B 340 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8227 (mt) REVERT: B 353 ARG cc_start: 0.9035 (mtt-85) cc_final: 0.8792 (mtt-85) REVERT: B 421 MET cc_start: 0.8808 (mtt) cc_final: 0.8588 (mtt) REVERT: A 14 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7844 (ttt90) REVERT: A 39 LYS cc_start: 0.8677 (mmtp) cc_final: 0.8153 (mmtp) REVERT: A 198 ASN cc_start: 0.8056 (t0) cc_final: 0.7621 (p0) REVERT: A 271 GLU cc_start: 0.8278 (tt0) cc_final: 0.8049 (tp30) REVERT: A 289 ASP cc_start: 0.8532 (t70) cc_final: 0.8150 (t0) REVERT: A 340 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8191 (mt) REVERT: C 39 LYS cc_start: 0.8700 (tppt) cc_final: 0.8279 (mmtp) REVERT: C 289 ASP cc_start: 0.8587 (t70) cc_final: 0.8206 (t0) outliers start: 37 outliers final: 30 residues processed: 199 average time/residue: 0.3574 time to fit residues: 94.2745 Evaluate side-chains 203 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 ASN Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 127 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN C 310 ASN C 326 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119941 restraints weight = 38225.973| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.45 r_work: 0.3309 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13536 Z= 0.134 Angle : 0.497 4.782 18364 Z= 0.255 Chirality : 0.044 0.147 2028 Planarity : 0.004 0.041 2400 Dihedral : 5.632 45.496 2008 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.69 % Allowed : 11.05 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.19), residues: 1680 helix: 0.79 (0.26), residues: 460 sheet: -1.62 (0.41), residues: 156 loop : -1.00 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 353 TYR 0.007 0.001 TYR C 283 PHE 0.008 0.001 PHE A 218 TRP 0.007 0.001 TRP A 284 HIS 0.004 0.001 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00323 (13536) covalent geometry : angle 0.49663 (18364) hydrogen bonds : bond 0.02883 ( 392) hydrogen bonds : angle 4.57825 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.733 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: D 39 LYS cc_start: 0.8704 (mmtp) cc_final: 0.8200 (mmtp) REVERT: D 198 ASN cc_start: 0.8055 (t0) cc_final: 0.7653 (p0) REVERT: D 289 ASP cc_start: 0.8553 (t70) cc_final: 0.8190 (t0) REVERT: D 303 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8006 (t0) REVERT: B 289 ASP cc_start: 0.8539 (t70) cc_final: 0.8176 (t0) REVERT: B 353 ARG cc_start: 0.9074 (mtt-85) cc_final: 0.8818 (mtt-85) REVERT: B 421 MET cc_start: 0.8817 (mtt) cc_final: 0.8603 (mtt) REVERT: A 14 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7864 (ttt90) REVERT: A 39 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8159 (mmtp) REVERT: A 198 ASN cc_start: 0.8061 (t0) cc_final: 0.7626 (p0) REVERT: A 289 ASP cc_start: 0.8550 (t70) cc_final: 0.8172 (t0) REVERT: C 39 LYS cc_start: 0.8716 (tppt) cc_final: 0.8302 (mmtp) REVERT: C 69 MET cc_start: 0.8965 (mtm) cc_final: 0.8619 (mtt) REVERT: C 289 ASP cc_start: 0.8590 (t70) cc_final: 0.8231 (t0) outliers start: 38 outliers final: 30 residues processed: 203 average time/residue: 0.3347 time to fit residues: 91.5846 Evaluate side-chains 198 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 326 HIS Chi-restraints excluded: chain C residue 340 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 31 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS C 326 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118746 restraints weight = 38040.305| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.50 r_work: 0.3293 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13536 Z= 0.144 Angle : 0.500 5.464 18364 Z= 0.256 Chirality : 0.045 0.147 2028 Planarity : 0.004 0.045 2400 Dihedral : 5.628 47.192 2008 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.62 % Allowed : 11.12 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1680 helix: 0.81 (0.26), residues: 460 sheet: -1.64 (0.40), residues: 156 loop : -1.02 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 353 TYR 0.007 0.001 TYR C 283 PHE 0.008 0.001 PHE C 218 TRP 0.007 0.001 TRP A 284 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00348 (13536) covalent geometry : angle 0.49966 (18364) hydrogen bonds : bond 0.02877 ( 392) hydrogen bonds : angle 4.59785 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.683 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: D 14 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7825 (ttt90) REVERT: D 39 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8131 (mmtp) REVERT: D 198 ASN cc_start: 0.8073 (t0) cc_final: 0.7646 (p0) REVERT: D 289 ASP cc_start: 0.8579 (t70) cc_final: 0.8212 (t0) REVERT: D 303 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.7938 (t0) REVERT: B 39 LYS cc_start: 0.8757 (tppt) cc_final: 0.8264 (mmtp) REVERT: B 108 MET cc_start: 0.7265 (mmm) cc_final: 0.6995 (mmp) REVERT: B 289 ASP cc_start: 0.8470 (t70) cc_final: 0.8144 (t0) REVERT: B 340 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8237 (mt) REVERT: B 353 ARG cc_start: 0.9033 (mtt-85) cc_final: 0.8783 (mtt-85) REVERT: A 14 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7918 (ttt90) REVERT: A 39 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8165 (mmtp) REVERT: A 198 ASN cc_start: 0.8084 (t0) cc_final: 0.7626 (p0) REVERT: A 289 ASP cc_start: 0.8485 (t70) cc_final: 0.8151 (t0) REVERT: C 14 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7880 (ttt90) REVERT: C 39 LYS cc_start: 0.8714 (tppt) cc_final: 0.8315 (mmtp) REVERT: C 69 MET cc_start: 0.8983 (mtm) cc_final: 0.8638 (mtt) REVERT: C 289 ASP cc_start: 0.8486 (t70) cc_final: 0.8171 (t0) outliers start: 37 outliers final: 29 residues processed: 201 average time/residue: 0.3491 time to fit residues: 93.7455 Evaluate side-chains 204 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116412 restraints weight = 38325.705| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.51 r_work: 0.3255 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13536 Z= 0.214 Angle : 0.534 6.214 18364 Z= 0.276 Chirality : 0.046 0.149 2028 Planarity : 0.005 0.048 2400 Dihedral : 5.778 46.101 2008 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.48 % Allowed : 11.19 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 1680 helix: 0.67 (0.26), residues: 456 sheet: -1.71 (0.40), residues: 156 loop : -1.08 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 353 TYR 0.007 0.001 TYR B 273 PHE 0.009 0.001 PHE A 218 TRP 0.008 0.001 TRP A 284 HIS 0.007 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00516 (13536) covalent geometry : angle 0.53418 (18364) hydrogen bonds : bond 0.03098 ( 392) hydrogen bonds : angle 4.75810 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3360 Ramachandran restraints generated. 1680 Oldfield, 0 Emsley, 1680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue TYR 114 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.515 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: D 14 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7905 (ttt90) REVERT: D 39 LYS cc_start: 0.8649 (mmtp) cc_final: 0.8106 (mmtp) REVERT: D 198 ASN cc_start: 0.8058 (t0) cc_final: 0.7596 (p0) REVERT: D 289 ASP cc_start: 0.8517 (t70) cc_final: 0.8187 (t0) REVERT: B 39 LYS cc_start: 0.8767 (tppt) cc_final: 0.8288 (mmtp) REVERT: B 108 MET cc_start: 0.7266 (mmm) cc_final: 0.6990 (mmp) REVERT: B 289 ASP cc_start: 0.8499 (t70) cc_final: 0.8186 (t0) REVERT: B 353 ARG cc_start: 0.9036 (mtt-85) cc_final: 0.8782 (mtt-85) REVERT: A 14 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7882 (ttt90) REVERT: A 39 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8084 (mmtp) REVERT: A 198 ASN cc_start: 0.8072 (t0) cc_final: 0.7593 (p0) REVERT: C 14 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7880 (ttt90) REVERT: C 108 MET cc_start: 0.7250 (mmm) cc_final: 0.6980 (mmp) outliers start: 35 outliers final: 28 residues processed: 193 average time/residue: 0.3734 time to fit residues: 96.1296 Evaluate side-chains 198 residues out of total 1456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 178 PHE Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 310 ASN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 71 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118884 restraints weight = 37837.311| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.46 r_work: 0.3296 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13536 Z= 0.130 Angle : 0.497 5.880 18364 Z= 0.254 Chirality : 0.044 0.148 2028 Planarity : 0.005 0.068 2400 Dihedral : 5.610 48.663 2008 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.12 % Allowed : 11.54 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1680 helix: 0.77 (0.26), residues: 460 sheet: -1.68 (0.40), residues: 156 loop : -1.05 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 353 TYR 0.006 0.001 TYR A 283 PHE 0.007 0.001 PHE C 218 TRP 0.007 0.001 TRP A 284 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00311 (13536) covalent geometry : angle 0.49702 (18364) hydrogen bonds : bond 0.02778 ( 392) hydrogen bonds : angle 4.57203 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6395.25 seconds wall clock time: 108 minutes 48.32 seconds (6528.32 seconds total)