Starting phenix.real_space_refine on Thu Aug 6 10:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io0_35603/08_2026/8io0_35603_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io0_35603/08_2026/8io0_35603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8io0_35603/08_2026/8io0_35603_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io0_35603/08_2026/8io0_35603_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8io0_35603/08_2026/8io0_35603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io0_35603/08_2026/8io0_35603.map" } resolution = 3.19 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= 0.008 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 9630 2.51 5 N 2503 2.21 5 O 2487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14728 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3654 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 18, 'TRANS': 454} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 163 Chain: "B" Number of atoms: 3662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3662 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 18, 'TRANS': 455} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 163 Chain: "C" Number of atoms: 3662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3662 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 18, 'TRANS': 455} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 163 Chain: "D" Number of atoms: 3662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3662 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 18, 'TRANS': 455} Chain breaks: 3 Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 14, 'ARG:plan': 13, 'HIS:plan': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna2p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna2p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNAv2': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 3.55, per 1000 atoms: 0.24 Number of scatterers: 14728 At special positions: 0 Unit cell: (100.2, 100.2, 122.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 4 15.00 O 2487 8.00 N 2503 7.00 C 9630 6.00 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: 1.14 Conformation dependent library (CDL) restraints added in 620.4 milliseconds 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 73.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.263A pdb=" N LEU A 53 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 90 through 117 removed outlier: 3.511A pdb=" N PHE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 123 through 146 removed outlier: 3.867A pdb=" N LEU A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.725A pdb=" N ILE A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.884A pdb=" N ILE A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 219 through 222 removed outlier: 3.637A pdb=" N LEU A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 222' Processing helix chain 'A' and resid 223 through 238 Processing helix chain 'A' and resid 245 through 276 removed outlier: 3.644A pdb=" N VAL A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS A 267 " --> pdb=" O HIS A 263 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.608A pdb=" N GLN A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 293 through 310 Processing helix chain 'A' and resid 321 through 351 removed outlier: 3.575A pdb=" N TRP A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 374 removed outlier: 3.538A pdb=" N TYR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.522A pdb=" N LEU A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 5.990A pdb=" N GLY A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.619A pdb=" N HIS A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.884A pdb=" N LEU A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 530 through 546 removed outlier: 3.792A pdb=" N ARG A 534 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 4.263A pdb=" N LEU B 53 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 66 Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 90 through 117 removed outlier: 3.511A pdb=" N PHE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 123 through 146 removed outlier: 3.867A pdb=" N LEU B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.725A pdb=" N ILE B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 182 through 191 removed outlier: 3.884A pdb=" N ILE B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 218 Processing helix chain 'B' and resid 219 through 222 removed outlier: 3.637A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 223 through 238 Processing helix chain 'B' and resid 245 through 276 removed outlier: 3.644A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) Proline residue: B 273 - end of helix removed outlier: 3.608A pdb=" N GLN B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 293 through 310 Processing helix chain 'B' and resid 321 through 351 removed outlier: 3.575A pdb=" N TRP B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 374 removed outlier: 3.538A pdb=" N TYR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B 374 " --> pdb=" O TYR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 392 Processing helix chain 'B' and resid 398 through 406 removed outlier: 3.522A pdb=" N LEU B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 5.990A pdb=" N GLY B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 removed outlier: 3.619A pdb=" N HIS B 431 " --> pdb=" O PRO B 427 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.884A pdb=" N LEU B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 530 through 546 removed outlier: 3.791A pdb=" N ARG B 534 " --> pdb=" O PRO B 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.263A pdb=" N LEU C 53 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 67 through 79 Processing helix chain 'C' and resid 90 through 117 removed outlier: 3.511A pdb=" N PHE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 123 through 146 removed outlier: 3.867A pdb=" N LEU C 141 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.725A pdb=" N ILE C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG C 165 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 182 through 191 removed outlier: 3.884A pdb=" N ILE C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 219 through 222 removed outlier: 3.637A pdb=" N LEU C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 222' Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 245 through 276 removed outlier: 3.644A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Proline residue: C 273 - end of helix removed outlier: 3.608A pdb=" N GLN C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 293 through 310 Processing helix chain 'C' and resid 321 through 351 removed outlier: 3.575A pdb=" N TRP C 326 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 374 removed outlier: 3.538A pdb=" N TYR C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS C 374 " --> pdb=" O TYR C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 392 Processing helix chain 'C' and resid 398 through 406 removed outlier: 3.522A pdb=" N LEU C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 removed outlier: 5.990A pdb=" N GLY C 421 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 432 removed outlier: 3.619A pdb=" N HIS C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.884A pdb=" N LEU C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 530 through 546 removed outlier: 3.792A pdb=" N ARG C 534 " --> pdb=" O PRO C 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.263A pdb=" N LEU D 53 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 90 through 117 removed outlier: 3.511A pdb=" N PHE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Proline residue: D 112 - end of helix Processing helix chain 'D' and resid 123 through 146 removed outlier: 3.867A pdb=" N LEU D 141 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.725A pdb=" N ILE D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ARG D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.884A pdb=" N ILE D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 218 Processing helix chain 'D' and resid 219 through 222 removed outlier: 3.637A pdb=" N LEU D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 222' Processing helix chain 'D' and resid 223 through 238 Processing helix chain 'D' and resid 245 through 276 removed outlier: 3.644A pdb=" N VAL D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS D 267 " --> pdb=" O HIS D 263 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.608A pdb=" N GLN D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 293 through 310 Processing helix chain 'D' and resid 321 through 351 removed outlier: 3.575A pdb=" N TRP D 326 " --> pdb=" O MET D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 374 removed outlier: 3.538A pdb=" N TYR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS D 374 " --> pdb=" O TYR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 392 Processing helix chain 'D' and resid 398 through 406 removed outlier: 3.522A pdb=" N LEU D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 removed outlier: 5.990A pdb=" N GLY D 421 " --> pdb=" O PHE D 417 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU D 422 " --> pdb=" O THR D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 432 removed outlier: 3.619A pdb=" N HIS D 431 " --> pdb=" O PRO D 427 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.884A pdb=" N LEU D 497 " --> pdb=" O GLU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 530 through 546 removed outlier: 3.791A pdb=" N ARG D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 449 Processing sheet with id=AA2, first strand: chain 'A' and resid 454 through 456 removed outlier: 6.699A pdb=" N LEU A 454 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA A 508 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 456 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 449 Processing sheet with id=AA4, first strand: chain 'B' and resid 454 through 456 removed outlier: 6.699A pdb=" N LEU B 454 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 508 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 456 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 445 through 449 Processing sheet with id=AA6, first strand: chain 'C' and resid 454 through 456 removed outlier: 6.699A pdb=" N LEU C 454 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA C 508 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL C 456 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 445 through 449 Processing sheet with id=AA8, first strand: chain 'D' and resid 454 through 456 removed outlier: 6.699A pdb=" N LEU D 454 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA D 508 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL D 456 " --> pdb=" O VAL D 506 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4574 1.34 - 1.46: 3876 1.46 - 1.58: 6490 1.58 - 1.70: 8 1.70 - 1.82: 176 Bond restraints: 15124 Sorted by residual: bond pdb=" C PRO A 124 " pdb=" N PRO A 125 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.25e-02 6.40e+03 4.32e+00 bond pdb=" C PRO C 124 " pdb=" N PRO C 125 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.25e-02 6.40e+03 4.32e+00 bond pdb=" C PRO D 124 " pdb=" N PRO D 125 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.25e-02 6.40e+03 4.32e+00 bond pdb=" C PRO B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.25e-02 6.40e+03 4.32e+00 bond pdb=" C4' CMP A 801 " pdb=" C5' CMP A 801 " ideal model delta sigma weight residual 1.524 1.485 0.039 2.00e-02 2.50e+03 3.78e+00 ... (remaining 15119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 19562 1.93 - 3.85: 839 3.85 - 5.78: 136 5.78 - 7.70: 56 7.70 - 9.63: 20 Bond angle restraints: 20613 Sorted by residual: angle pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" C PRO B 124 " ideal model delta sigma weight residual 110.70 115.45 -4.75 1.22e+00 6.72e-01 1.52e+01 angle pdb=" N PRO A 124 " pdb=" CA PRO A 124 " pdb=" C PRO A 124 " ideal model delta sigma weight residual 110.70 115.45 -4.75 1.22e+00 6.72e-01 1.52e+01 angle pdb=" N PRO D 124 " pdb=" CA PRO D 124 " pdb=" C PRO D 124 " ideal model delta sigma weight residual 110.70 115.45 -4.75 1.22e+00 6.72e-01 1.52e+01 angle pdb=" N PRO C 124 " pdb=" CA PRO C 124 " pdb=" C PRO C 124 " ideal model delta sigma weight residual 110.70 115.45 -4.75 1.22e+00 6.72e-01 1.52e+01 angle pdb=" CA PRO B 124 " pdb=" C PRO B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 117.93 122.39 -4.46 1.20e+00 6.94e-01 1.38e+01 ... (remaining 20608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 8743 34.79 - 69.58: 16 69.58 - 104.36: 16 104.36 - 139.15: 0 139.15 - 173.94: 8 Dihedral angle restraints: 8783 sinusoidal: 3230 harmonic: 5553 Sorted by residual: dihedral pdb=" C3' CMP D 801 " pdb=" O3' CMP D 801 " pdb=" P CMP D 801 " pdb=" O1P CMP D 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.94 -173.94 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3' CMP C 801 " pdb=" O3' CMP C 801 " pdb=" P CMP C 801 " pdb=" O1P CMP C 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.94 -173.94 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3' CMP B 801 " pdb=" O3' CMP B 801 " pdb=" P CMP B 801 " pdb=" O1P CMP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 113.94 -173.94 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 8780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1878 0.063 - 0.127: 452 0.127 - 0.190: 44 0.190 - 0.253: 0 0.253 - 0.316: 4 Chirality restraints: 2378 Sorted by residual: chirality pdb=" C1' CMP A 801 " pdb=" C2' CMP A 801 " pdb=" N9 CMP A 801 " pdb=" O4' CMP A 801 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1' CMP B 801 " pdb=" C2' CMP B 801 " pdb=" N9 CMP B 801 " pdb=" O4' CMP B 801 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1' CMP C 801 " pdb=" C2' CMP C 801 " pdb=" N9 CMP C 801 " pdb=" O4' CMP C 801 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2375 not shown) Planarity restraints: 2543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 234 " -0.034 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP B 234 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 234 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 234 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 234 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 234 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 234 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 234 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 234 " -0.034 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP D 234 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP D 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 234 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 234 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 234 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 234 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 234 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 234 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " -0.034 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP A 234 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " -0.002 2.00e-02 2.50e+03 ... (remaining 2540 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4024 2.80 - 3.32: 13646 3.32 - 3.85: 23970 3.85 - 4.37: 25612 4.37 - 4.90: 45142 Nonbonded interactions: 112394 Sorted by model distance: nonbonded pdb=" O VAL C 475 " pdb=" OG1 THR C 483 " model vdw 2.274 3.040 nonbonded pdb=" O VAL D 475 " pdb=" OG1 THR D 483 " model vdw 2.274 3.040 nonbonded pdb=" O VAL B 475 " pdb=" OG1 THR B 483 " model vdw 2.274 3.040 nonbonded pdb=" O VAL A 475 " pdb=" OG1 THR A 483 " model vdw 2.274 3.040 nonbonded pdb=" O ARG B 167 " pdb=" OG1 THR B 171 " model vdw 2.329 3.040 ... (remaining 112389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 50 through 475 or resid 483 through 801)) selection = (chain 'C' and (resid 50 through 475 or resid 483 through 801)) selection = (chain 'D' and (resid 50 through 475 or resid 483 through 801)) } 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.000 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 15124 Z= 0.370 Angle : 0.996 9.629 20613 Z= 0.539 Chirality : 0.054 0.316 2378 Planarity : 0.007 0.062 2543 Dihedral : 11.419 173.940 5185 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.27 % Allowed : 1.08 % Favored : 98.64 % 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: -2.04 (0.16), residues: 1863 helix: -1.00 (0.12), residues: 1244 sheet: 0.41 (0.64), residues: 48 loop : -2.01 (0.23), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 420 TYR 0.024 0.003 TYR D 511 PHE 0.048 0.003 PHE D 238 TRP 0.053 0.003 TRP B 234 HIS 0.016 0.003 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.37 (15124) covalent geometry : angle 0.99568 / 0.54 (20613) hydrogen bonds : bond 0.15747 / 10.98 ( 970) hydrogen bonds : angle 5.81752 / 4.23 ( 2853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.571 Fit side-chains REVERT: A 100 MET cc_start: 0.8915 (mmm) cc_final: 0.8283 (tpp) REVERT: A 257 MET cc_start: 0.9138 (tpp) cc_final: 0.8837 (tpp) REVERT: A 365 LYS cc_start: 0.9295 (mmtt) cc_final: 0.9090 (tttt) REVERT: A 386 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9087 (mt-10) REVERT: A 389 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8169 (mt-10) REVERT: A 395 LYS cc_start: 0.8503 (mttt) cc_final: 0.7895 (mtpt) REVERT: A 443 LYS cc_start: 0.9623 (mttt) cc_final: 0.9309 (mtmt) REVERT: A 465 MET cc_start: 0.9347 (ttm) cc_final: 0.9077 (ttt) REVERT: A 485 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8407 (pt) REVERT: A 537 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9267 (mp0) REVERT: A 541 MET cc_start: 0.9709 (mmm) cc_final: 0.9432 (mmm) REVERT: B 100 MET cc_start: 0.8910 (mmm) cc_final: 0.8283 (tpp) REVERT: B 257 MET cc_start: 0.9138 (tpp) cc_final: 0.8838 (tpp) REVERT: B 365 LYS cc_start: 0.9295 (mmtt) cc_final: 0.9091 (tttt) REVERT: B 386 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9086 (mt-10) REVERT: B 389 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8167 (mt-10) REVERT: B 395 LYS cc_start: 0.8498 (mttt) cc_final: 0.7891 (mtpt) REVERT: B 443 LYS cc_start: 0.9625 (mttt) cc_final: 0.9315 (mtmt) REVERT: B 465 MET cc_start: 0.9349 (ttm) cc_final: 0.9078 (ttt) REVERT: B 485 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8408 (pt) REVERT: B 537 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9265 (mp0) REVERT: B 541 MET cc_start: 0.9708 (mmm) cc_final: 0.9430 (mmm) REVERT: C 100 MET cc_start: 0.8909 (mmm) cc_final: 0.8277 (tpp) REVERT: C 257 MET cc_start: 0.9141 (tpp) cc_final: 0.8839 (tpp) REVERT: C 365 LYS cc_start: 0.9297 (mmtt) cc_final: 0.9091 (tttt) REVERT: C 386 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9091 (mt-10) REVERT: C 389 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8166 (mt-10) REVERT: C 395 LYS cc_start: 0.8500 (mttt) cc_final: 0.7895 (mtpt) REVERT: C 443 LYS cc_start: 0.9622 (mttt) cc_final: 0.9308 (mtmt) REVERT: C 465 MET cc_start: 0.9345 (ttm) cc_final: 0.9075 (ttt) REVERT: C 485 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8411 (pt) REVERT: C 537 GLU cc_start: 0.9528 (mt-10) cc_final: 0.9265 (mp0) REVERT: C 541 MET cc_start: 0.9711 (mmm) cc_final: 0.9434 (mmm) REVERT: D 100 MET cc_start: 0.8906 (mmm) cc_final: 0.8274 (tpp) REVERT: D 257 MET cc_start: 0.9139 (tpp) cc_final: 0.8839 (tpp) REVERT: D 365 LYS cc_start: 0.9294 (mmtt) cc_final: 0.9089 (tttt) REVERT: D 386 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9089 (mt-10) REVERT: D 389 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8164 (mt-10) REVERT: D 395 LYS cc_start: 0.8493 (mttt) cc_final: 0.7886 (mtpt) REVERT: D 443 LYS cc_start: 0.9623 (mttt) cc_final: 0.9313 (mtmt) REVERT: D 465 MET cc_start: 0.9349 (ttm) cc_final: 0.9078 (ttt) REVERT: D 485 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8408 (pt) REVERT: D 537 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9264 (mp0) REVERT: D 541 MET cc_start: 0.9708 (mmm) cc_final: 0.9432 (mmm) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.1630 time to fit residues: 41.7258 Evaluate side-chains 109 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN A 130 ASN A 292 HIS A 308 HIS A 470 HIS A 521 HIS B 107 ASN B 130 ASN B 292 HIS B 308 HIS B 470 HIS B 521 HIS C 107 ASN C 130 ASN C 292 HIS C 308 HIS C 470 HIS C 521 HIS D 107 ASN D 130 ASN D 292 HIS D 308 HIS D 470 HIS D 521 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.063844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046207 restraints weight = 64476.823| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.92 r_work: 0.2735 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15124 Z= 0.140 Angle : 0.615 8.575 20613 Z= 0.301 Chirality : 0.039 0.166 2378 Planarity : 0.004 0.046 2543 Dihedral : 11.052 156.538 2103 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.27 % Allowed : 5.90 % Favored : 93.83 % 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: 0.64 (0.19), residues: 1863 helix: 1.19 (0.14), residues: 1292 sheet: 1.20 (0.59), residues: 48 loop : -1.56 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 463 TYR 0.011 0.001 TYR B 95 PHE 0.011 0.001 PHE D 270 TRP 0.016 0.001 TRP A 264 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (15124) covalent geometry : angle 0.61473 / 0.30 (20613) hydrogen bonds : bond 0.04295 / 2.90 ( 970) hydrogen bonds : angle 3.84525 / 2.82 ( 2853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9160 (mmm) cc_final: 0.8662 (tpp) REVERT: A 257 MET cc_start: 0.9428 (tpp) cc_final: 0.9223 (tpp) REVERT: A 395 LYS cc_start: 0.8220 (mttt) cc_final: 0.7636 (mtpt) REVERT: A 426 MET cc_start: 0.8330 (mmm) cc_final: 0.8062 (tpp) REVERT: A 465 MET cc_start: 0.9446 (ttm) cc_final: 0.9138 (ttt) REVERT: A 485 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8143 (pt) REVERT: A 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9494 (mmm) REVERT: B 100 MET cc_start: 0.9167 (mmm) cc_final: 0.8675 (tpp) REVERT: B 257 MET cc_start: 0.9419 (tpp) cc_final: 0.9211 (tpp) REVERT: B 395 LYS cc_start: 0.8208 (mttt) cc_final: 0.7634 (mtpt) REVERT: B 426 MET cc_start: 0.8332 (mmm) cc_final: 0.8066 (tpp) REVERT: B 465 MET cc_start: 0.9436 (ttm) cc_final: 0.9119 (ttt) REVERT: B 485 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8261 (pt) REVERT: B 541 MET cc_start: 0.9767 (mmm) cc_final: 0.9484 (mmm) REVERT: C 100 MET cc_start: 0.9152 (mmm) cc_final: 0.8655 (tpp) REVERT: C 257 MET cc_start: 0.9428 (tpp) cc_final: 0.9222 (tpp) REVERT: C 395 LYS cc_start: 0.8219 (mttt) cc_final: 0.7643 (mtpt) REVERT: C 426 MET cc_start: 0.8327 (mmm) cc_final: 0.8063 (tpp) REVERT: C 465 MET cc_start: 0.9441 (ttm) cc_final: 0.9131 (ttt) REVERT: C 485 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8261 (pt) REVERT: C 541 MET cc_start: 0.9768 (mmm) cc_final: 0.9483 (mmm) REVERT: D 100 MET cc_start: 0.9152 (mmm) cc_final: 0.8662 (tpp) REVERT: D 257 MET cc_start: 0.9426 (tpp) cc_final: 0.9219 (tpp) REVERT: D 395 LYS cc_start: 0.8217 (mttt) cc_final: 0.7642 (mtpt) REVERT: D 426 MET cc_start: 0.8327 (mmm) cc_final: 0.8062 (tpp) REVERT: D 465 MET cc_start: 0.9441 (ttm) cc_final: 0.9127 (ttt) REVERT: D 485 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8263 (pt) REVERT: D 541 MET cc_start: 0.9761 (mmm) cc_final: 0.9474 (mmm) outliers start: 4 outliers final: 0 residues processed: 124 average time/residue: 0.1311 time to fit residues: 24.0162 Evaluate side-chains 116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 79 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.063563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.046018 restraints weight = 65101.456| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.97 r_work: 0.2727 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15124 Z= 0.145 Angle : 0.588 8.266 20613 Z= 0.282 Chirality : 0.039 0.152 2378 Planarity : 0.004 0.047 2543 Dihedral : 10.827 157.125 2103 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.81 % Allowed : 5.97 % Favored : 93.22 % 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: 1.89 (0.19), residues: 1863 helix: 2.12 (0.14), residues: 1296 sheet: 1.83 (0.61), residues: 48 loop : -1.09 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 463 TYR 0.011 0.001 TYR B 511 PHE 0.011 0.001 PHE D 270 TRP 0.013 0.001 TRP C 264 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (15124) covalent geometry : angle 0.58762 / 0.28 (20613) hydrogen bonds : bond 0.03733 / 2.54 ( 970) hydrogen bonds : angle 3.46755 / 2.53 ( 2853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9169 (mmm) cc_final: 0.8963 (mmm) REVERT: A 257 MET cc_start: 0.9407 (tpp) cc_final: 0.9201 (tpp) REVERT: A 365 LYS cc_start: 0.9420 (tttt) cc_final: 0.9169 (tttt) REVERT: A 426 MET cc_start: 0.8459 (mmm) cc_final: 0.8166 (tpp) REVERT: A 485 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8156 (pp) REVERT: A 531 MET cc_start: 0.9065 (pmm) cc_final: 0.8603 (pmm) REVERT: A 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9510 (mmm) REVERT: B 100 MET cc_start: 0.9180 (mmm) cc_final: 0.8976 (mmm) REVERT: B 257 MET cc_start: 0.9392 (tpp) cc_final: 0.9183 (tpp) REVERT: B 365 LYS cc_start: 0.9421 (tttt) cc_final: 0.9170 (tttt) REVERT: B 426 MET cc_start: 0.8457 (mmm) cc_final: 0.8166 (tpp) REVERT: B 485 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8409 (pp) REVERT: B 531 MET cc_start: 0.9066 (pmm) cc_final: 0.8604 (pmm) REVERT: B 541 MET cc_start: 0.9778 (mmm) cc_final: 0.9504 (mmm) REVERT: C 100 MET cc_start: 0.9170 (mmm) cc_final: 0.8962 (mmm) REVERT: C 257 MET cc_start: 0.9373 (tpp) cc_final: 0.9154 (tpp) REVERT: C 365 LYS cc_start: 0.9422 (tttt) cc_final: 0.9171 (tttt) REVERT: C 426 MET cc_start: 0.8462 (mmm) cc_final: 0.8173 (tpp) REVERT: C 485 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8410 (pp) REVERT: C 531 MET cc_start: 0.9078 (pmm) cc_final: 0.8620 (pmm) REVERT: C 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9501 (mmm) REVERT: D 100 MET cc_start: 0.9168 (mmm) cc_final: 0.8965 (mmm) REVERT: D 257 MET cc_start: 0.9381 (tpp) cc_final: 0.9168 (tpp) REVERT: D 365 LYS cc_start: 0.9422 (tttt) cc_final: 0.9169 (tttt) REVERT: D 426 MET cc_start: 0.8462 (mmm) cc_final: 0.8173 (tpp) REVERT: D 485 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8409 (pp) REVERT: D 531 MET cc_start: 0.9080 (pmm) cc_final: 0.8621 (pmm) REVERT: D 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9499 (mmm) outliers start: 12 outliers final: 4 residues processed: 120 average time/residue: 0.1421 time to fit residues: 25.0123 Evaluate side-chains 114 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 234 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 87 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.062900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045364 restraints weight = 65773.604| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.98 r_work: 0.2706 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15124 Z= 0.161 Angle : 0.590 8.409 20613 Z= 0.284 Chirality : 0.039 0.157 2378 Planarity : 0.003 0.041 2543 Dihedral : 10.747 156.387 2103 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.81 % Allowed : 4.88 % Favored : 94.31 % 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: 2.36 (0.20), residues: 1863 helix: 2.46 (0.14), residues: 1296 sheet: 2.09 (0.62), residues: 48 loop : -0.88 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 507 TYR 0.011 0.001 TYR C 511 PHE 0.011 0.001 PHE A 270 TRP 0.011 0.001 TRP A 264 HIS 0.004 0.001 HIS D 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15124) covalent geometry : angle 0.59035 / 0.28 (20613) hydrogen bonds : bond 0.03741 / 2.54 ( 970) hydrogen bonds : angle 3.44078 / 2.51 ( 2853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9186 (mmm) cc_final: 0.8909 (mmm) REVERT: A 257 MET cc_start: 0.9403 (tpp) cc_final: 0.9196 (tpp) REVERT: A 365 LYS cc_start: 0.9408 (tttt) cc_final: 0.9189 (tttt) REVERT: A 395 LYS cc_start: 0.8421 (mttt) cc_final: 0.7977 (mtmm) REVERT: A 443 LYS cc_start: 0.9607 (mttt) cc_final: 0.9355 (mtmm) REVERT: A 485 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8191 (pp) REVERT: A 531 MET cc_start: 0.9031 (pmm) cc_final: 0.8633 (pmm) REVERT: A 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9511 (mmm) REVERT: B 100 MET cc_start: 0.9196 (mmm) cc_final: 0.8921 (mmm) REVERT: B 257 MET cc_start: 0.9396 (tpp) cc_final: 0.9187 (tpp) REVERT: B 365 LYS cc_start: 0.9408 (tttt) cc_final: 0.9191 (tttt) REVERT: B 395 LYS cc_start: 0.8420 (mttt) cc_final: 0.7982 (mtmm) REVERT: B 443 LYS cc_start: 0.9608 (mttt) cc_final: 0.9359 (mtmm) REVERT: B 485 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8458 (pp) REVERT: B 531 MET cc_start: 0.9033 (pmm) cc_final: 0.8636 (pmm) REVERT: B 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9505 (mmm) REVERT: C 100 MET cc_start: 0.9185 (mmm) cc_final: 0.8907 (mmm) REVERT: C 257 MET cc_start: 0.9394 (tpp) cc_final: 0.9182 (tpp) REVERT: C 365 LYS cc_start: 0.9411 (tttt) cc_final: 0.9192 (tttt) REVERT: C 395 LYS cc_start: 0.8417 (mttt) cc_final: 0.7981 (mtmm) REVERT: C 443 LYS cc_start: 0.9610 (mttt) cc_final: 0.9359 (mtmm) REVERT: C 485 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8461 (pp) REVERT: C 531 MET cc_start: 0.9042 (pmm) cc_final: 0.8646 (pmm) REVERT: C 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9503 (mmm) REVERT: D 100 MET cc_start: 0.9186 (mmm) cc_final: 0.8913 (mmm) REVERT: D 257 MET cc_start: 0.9407 (tpp) cc_final: 0.9200 (tpp) REVERT: D 365 LYS cc_start: 0.9411 (tttt) cc_final: 0.9194 (tttt) REVERT: D 395 LYS cc_start: 0.8423 (mttt) cc_final: 0.7990 (mtmm) REVERT: D 443 LYS cc_start: 0.9611 (mttt) cc_final: 0.9356 (mtmm) REVERT: D 485 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8458 (pp) REVERT: D 531 MET cc_start: 0.9040 (pmm) cc_final: 0.8643 (pmm) REVERT: D 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9506 (mmm) outliers start: 12 outliers final: 4 residues processed: 116 average time/residue: 0.1286 time to fit residues: 21.4517 Evaluate side-chains 112 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 234 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 50 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.061769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.044346 restraints weight = 65354.855| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.89 r_work: 0.2667 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15124 Z= 0.198 Angle : 0.624 8.596 20613 Z= 0.302 Chirality : 0.040 0.155 2378 Planarity : 0.004 0.042 2543 Dihedral : 10.709 155.572 2103 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.08 % Allowed : 5.42 % Favored : 93.49 % 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: 2.52 (0.20), residues: 1863 helix: 2.54 (0.14), residues: 1296 sheet: 2.26 (0.66), residues: 48 loop : -0.73 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 420 TYR 0.015 0.001 TYR A 511 PHE 0.011 0.001 PHE A 270 TRP 0.009 0.001 TRP C 264 HIS 0.004 0.001 HIS C 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (15124) covalent geometry : angle 0.62377 / 0.30 (20613) hydrogen bonds : bond 0.04105 / 2.79 ( 970) hydrogen bonds : angle 3.54379 / 2.59 ( 2853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 LYS cc_start: 0.9442 (tttt) cc_final: 0.9221 (tttt) REVERT: A 395 LYS cc_start: 0.8555 (mttt) cc_final: 0.8094 (mtmm) REVERT: A 443 LYS cc_start: 0.9617 (mttt) cc_final: 0.9340 (mtmm) REVERT: A 485 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 494 ILE cc_start: 0.9477 (OUTLIER) cc_final: 0.9240 (pt) REVERT: A 531 MET cc_start: 0.9035 (pmm) cc_final: 0.8730 (pmm) REVERT: A 532 MET cc_start: 0.9466 (mmm) cc_final: 0.9194 (mmp) REVERT: A 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9513 (mmm) REVERT: B 257 MET cc_start: 0.9437 (tpp) cc_final: 0.9236 (tpp) REVERT: B 365 LYS cc_start: 0.9441 (tttt) cc_final: 0.9218 (tttt) REVERT: B 395 LYS cc_start: 0.8554 (mttt) cc_final: 0.8097 (mtmm) REVERT: B 443 LYS cc_start: 0.9635 (mttt) cc_final: 0.9407 (mtmm) REVERT: B 485 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8454 (pp) REVERT: B 494 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9236 (pt) REVERT: B 531 MET cc_start: 0.9039 (pmm) cc_final: 0.8710 (pmm) REVERT: B 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9512 (mmm) REVERT: C 257 MET cc_start: 0.9440 (tpp) cc_final: 0.9240 (tpp) REVERT: C 365 LYS cc_start: 0.9446 (tttt) cc_final: 0.9225 (tttt) REVERT: C 395 LYS cc_start: 0.8550 (mttt) cc_final: 0.8098 (mtmm) REVERT: C 443 LYS cc_start: 0.9637 (mttt) cc_final: 0.9404 (mtmm) REVERT: C 485 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8456 (pp) REVERT: C 494 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9239 (pt) REVERT: C 531 MET cc_start: 0.9041 (pmm) cc_final: 0.8713 (pmm) REVERT: C 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9504 (mmm) REVERT: D 365 LYS cc_start: 0.9444 (tttt) cc_final: 0.9222 (tttt) REVERT: D 395 LYS cc_start: 0.8554 (mttt) cc_final: 0.8101 (mtmm) REVERT: D 443 LYS cc_start: 0.9637 (mttt) cc_final: 0.9404 (mtmm) REVERT: D 485 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8454 (pp) REVERT: D 494 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9239 (pt) REVERT: D 531 MET cc_start: 0.9040 (pmm) cc_final: 0.8712 (pmm) REVERT: D 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9511 (mmm) outliers start: 16 outliers final: 8 residues processed: 124 average time/residue: 0.1077 time to fit residues: 20.2406 Evaluate side-chains 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 234 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 133 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.063420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.045969 restraints weight = 65215.772| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.93 r_work: 0.2715 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15124 Z= 0.119 Angle : 0.575 8.262 20613 Z= 0.269 Chirality : 0.038 0.153 2378 Planarity : 0.003 0.043 2543 Dihedral : 10.743 157.469 2103 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.08 % Allowed : 5.97 % Favored : 92.95 % 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: 2.79 (0.20), residues: 1863 helix: 2.71 (0.14), residues: 1296 sheet: 2.45 (0.70), residues: 48 loop : -0.56 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 420 TYR 0.009 0.001 TYR C 364 PHE 0.009 0.001 PHE A 270 TRP 0.013 0.001 TRP B 264 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15124) covalent geometry : angle 0.57469 / 0.27 (20613) hydrogen bonds : bond 0.03371 / 2.28 ( 970) hydrogen bonds : angle 3.30966 / 2.42 ( 2853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 100 MET cc_start: 0.9041 (mmp) cc_final: 0.8673 (mmm) REVERT: A 240 MET cc_start: 0.8453 (tpp) cc_final: 0.8086 (tpp) REVERT: A 365 LYS cc_start: 0.9439 (tttt) cc_final: 0.9200 (tttt) REVERT: A 395 LYS cc_start: 0.8415 (mttt) cc_final: 0.8008 (mtmm) REVERT: A 426 MET cc_start: 0.8479 (mmm) cc_final: 0.8157 (tpp) REVERT: A 485 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8196 (pp) REVERT: A 494 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9135 (pt) REVERT: A 531 MET cc_start: 0.9049 (pmm) cc_final: 0.8819 (pmm) REVERT: A 532 MET cc_start: 0.9443 (mmm) cc_final: 0.9189 (mmp) REVERT: A 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9493 (mmm) REVERT: B 100 MET cc_start: 0.9051 (mmp) cc_final: 0.8686 (mmm) REVERT: B 240 MET cc_start: 0.8459 (tpp) cc_final: 0.8094 (tpp) REVERT: B 257 MET cc_start: 0.9391 (tpp) cc_final: 0.9190 (tpp) REVERT: B 365 LYS cc_start: 0.9438 (tttt) cc_final: 0.9197 (tttt) REVERT: B 395 LYS cc_start: 0.8410 (mttt) cc_final: 0.8004 (mtmm) REVERT: B 426 MET cc_start: 0.8487 (mmm) cc_final: 0.8165 (tpp) REVERT: B 443 LYS cc_start: 0.9599 (mttt) cc_final: 0.9353 (mtmm) REVERT: B 485 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8482 (pp) REVERT: B 494 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9127 (pt) REVERT: B 531 MET cc_start: 0.9057 (pmm) cc_final: 0.8837 (pmm) REVERT: B 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9490 (mmm) REVERT: C 100 MET cc_start: 0.9038 (mmp) cc_final: 0.8673 (mmm) REVERT: C 240 MET cc_start: 0.8444 (tpp) cc_final: 0.8075 (tpp) REVERT: C 257 MET cc_start: 0.9392 (tpp) cc_final: 0.9190 (tpp) REVERT: C 365 LYS cc_start: 0.9441 (tttt) cc_final: 0.9202 (tttt) REVERT: C 395 LYS cc_start: 0.8406 (mttt) cc_final: 0.8001 (mtmm) REVERT: C 426 MET cc_start: 0.8488 (mmm) cc_final: 0.8171 (tpp) REVERT: C 443 LYS cc_start: 0.9601 (mttt) cc_final: 0.9351 (mtmm) REVERT: C 485 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8484 (pp) REVERT: C 494 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9132 (pt) REVERT: C 531 MET cc_start: 0.9067 (pmm) cc_final: 0.8846 (pmm) REVERT: C 541 MET cc_start: 0.9769 (mmm) cc_final: 0.9485 (mmm) REVERT: D 100 MET cc_start: 0.9041 (mmp) cc_final: 0.8678 (mmm) REVERT: D 240 MET cc_start: 0.8443 (tpp) cc_final: 0.8073 (tpp) REVERT: D 365 LYS cc_start: 0.9440 (tttt) cc_final: 0.9201 (tttt) REVERT: D 395 LYS cc_start: 0.8413 (mttt) cc_final: 0.8011 (mtmm) REVERT: D 426 MET cc_start: 0.8491 (mmm) cc_final: 0.8171 (tpp) REVERT: D 443 LYS cc_start: 0.9598 (mttt) cc_final: 0.9347 (mtmm) REVERT: D 485 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8481 (pp) REVERT: D 494 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9134 (pt) REVERT: D 531 MET cc_start: 0.9058 (pmm) cc_final: 0.8839 (pmm) REVERT: D 541 MET cc_start: 0.9772 (mmm) cc_final: 0.9489 (mmm) outliers start: 16 outliers final: 4 residues processed: 127 average time/residue: 0.0999 time to fit residues: 19.1665 Evaluate side-chains 116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 40 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 138 optimal weight: 9.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.064029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046650 restraints weight = 64589.854| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.90 r_work: 0.2733 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15124 Z= 0.099 Angle : 0.549 8.112 20613 Z= 0.255 Chirality : 0.037 0.149 2378 Planarity : 0.003 0.043 2543 Dihedral : 10.628 157.548 2103 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 6.10 % Favored : 92.81 % 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: 2.97 (0.20), residues: 1863 helix: 2.81 (0.14), residues: 1296 sheet: 2.73 (0.72), residues: 48 loop : -0.39 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.008 0.001 TYR C 364 PHE 0.010 0.001 PHE A 270 TRP 0.013 0.001 TRP B 264 HIS 0.002 0.000 HIS C 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (15124) covalent geometry : angle 0.54947 / 0.26 (20613) hydrogen bonds : bond 0.02975 / 2.02 ( 970) hydrogen bonds : angle 3.18511 / 2.33 ( 2853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9057 (mmp) cc_final: 0.8707 (mmm) REVERT: A 240 MET cc_start: 0.8641 (tpp) cc_final: 0.8282 (tpp) REVERT: A 365 LYS cc_start: 0.9436 (tttt) cc_final: 0.9193 (tttt) REVERT: A 395 LYS cc_start: 0.8380 (mttt) cc_final: 0.8072 (mtmm) REVERT: A 465 MET cc_start: 0.9054 (ttt) cc_final: 0.8838 (ttp) REVERT: A 485 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8177 (pp) REVERT: A 494 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8965 (pt) REVERT: A 532 MET cc_start: 0.9423 (mmm) cc_final: 0.9151 (mmp) REVERT: A 541 MET cc_start: 0.9778 (mmm) cc_final: 0.9494 (mmm) REVERT: B 100 MET cc_start: 0.9063 (mmp) cc_final: 0.8709 (mmm) REVERT: B 240 MET cc_start: 0.8640 (tpp) cc_final: 0.8282 (tpp) REVERT: B 257 MET cc_start: 0.9341 (tpp) cc_final: 0.9131 (tpp) REVERT: B 365 LYS cc_start: 0.9434 (tttt) cc_final: 0.9190 (tttt) REVERT: B 395 LYS cc_start: 0.8376 (mttt) cc_final: 0.8069 (mtmm) REVERT: B 465 MET cc_start: 0.9036 (ttt) cc_final: 0.8815 (ttp) REVERT: B 485 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8493 (pp) REVERT: B 494 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8977 (pt) REVERT: B 531 MET cc_start: 0.9052 (pmm) cc_final: 0.8838 (pmm) REVERT: B 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9496 (mmm) REVERT: C 100 MET cc_start: 0.9053 (mmp) cc_final: 0.8702 (mmm) REVERT: C 240 MET cc_start: 0.8597 (tpp) cc_final: 0.8246 (tpp) REVERT: C 257 MET cc_start: 0.9348 (tpp) cc_final: 0.9137 (tpp) REVERT: C 365 LYS cc_start: 0.9435 (tttt) cc_final: 0.9192 (tttt) REVERT: C 395 LYS cc_start: 0.8370 (mttt) cc_final: 0.8066 (mtmm) REVERT: C 465 MET cc_start: 0.9053 (ttt) cc_final: 0.8839 (ttp) REVERT: C 485 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8494 (pp) REVERT: C 494 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8978 (pt) REVERT: C 531 MET cc_start: 0.9055 (pmm) cc_final: 0.8842 (pmm) REVERT: C 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9486 (mmm) REVERT: D 100 MET cc_start: 0.9061 (mmp) cc_final: 0.8714 (mmm) REVERT: D 240 MET cc_start: 0.8606 (tpp) cc_final: 0.8258 (tpp) REVERT: D 365 LYS cc_start: 0.9436 (tttt) cc_final: 0.9192 (tttt) REVERT: D 395 LYS cc_start: 0.8369 (mttt) cc_final: 0.8067 (mtmm) REVERT: D 465 MET cc_start: 0.9046 (ttt) cc_final: 0.8830 (ttp) REVERT: D 485 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8491 (pp) REVERT: D 494 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8980 (pt) REVERT: D 531 MET cc_start: 0.9044 (pmm) cc_final: 0.8832 (pmm) REVERT: D 541 MET cc_start: 0.9778 (mmm) cc_final: 0.9495 (mmm) outliers start: 16 outliers final: 4 residues processed: 120 average time/residue: 0.1167 time to fit residues: 21.0478 Evaluate side-chains 112 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 105 optimal weight: 20.0000 chunk 163 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 151 optimal weight: 0.0030 chunk 123 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.064572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047125 restraints weight = 65311.603| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.95 r_work: 0.2750 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15124 Z= 0.091 Angle : 0.550 8.618 20613 Z= 0.253 Chirality : 0.037 0.145 2378 Planarity : 0.003 0.043 2543 Dihedral : 10.541 157.393 2103 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.54 % Allowed : 6.71 % Favored : 92.75 % 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: 3.08 (0.20), residues: 1863 helix: 2.88 (0.14), residues: 1296 sheet: 2.84 (0.73), residues: 48 loop : -0.33 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.007 0.001 TYR A 364 PHE 0.009 0.001 PHE A 270 TRP 0.012 0.001 TRP B 264 HIS 0.003 0.000 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (15124) covalent geometry : angle 0.55026 / 0.25 (20613) hydrogen bonds : bond 0.02798 / 1.89 ( 970) hydrogen bonds : angle 3.12803 / 2.29 ( 2853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9025 (mmp) cc_final: 0.8683 (mmm) REVERT: A 240 MET cc_start: 0.8641 (tpp) cc_final: 0.8277 (tpp) REVERT: A 365 LYS cc_start: 0.9426 (tttt) cc_final: 0.9179 (tttt) REVERT: A 395 LYS cc_start: 0.8322 (mttt) cc_final: 0.8035 (mtmm) REVERT: A 485 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8148 (pp) REVERT: A 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9486 (mmm) REVERT: B 100 MET cc_start: 0.9034 (mmp) cc_final: 0.8691 (mmm) REVERT: B 240 MET cc_start: 0.8646 (tpp) cc_final: 0.8285 (tpp) REVERT: B 257 MET cc_start: 0.9312 (tpp) cc_final: 0.9100 (tpp) REVERT: B 365 LYS cc_start: 0.9428 (tttt) cc_final: 0.9179 (tttt) REVERT: B 395 LYS cc_start: 0.8316 (mttt) cc_final: 0.8033 (mtmm) REVERT: B 485 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8488 (pp) REVERT: B 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9487 (mmm) REVERT: C 100 MET cc_start: 0.9028 (mmp) cc_final: 0.8685 (mmm) REVERT: C 240 MET cc_start: 0.8631 (tpp) cc_final: 0.8263 (tpp) REVERT: C 257 MET cc_start: 0.9326 (tpp) cc_final: 0.9114 (tpp) REVERT: C 365 LYS cc_start: 0.9429 (tttt) cc_final: 0.9182 (tttt) REVERT: C 395 LYS cc_start: 0.8317 (mttt) cc_final: 0.8032 (mtmm) REVERT: C 485 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8489 (pp) REVERT: C 541 MET cc_start: 0.9768 (mmm) cc_final: 0.9477 (mmm) REVERT: D 100 MET cc_start: 0.9033 (mmp) cc_final: 0.8693 (mmm) REVERT: D 240 MET cc_start: 0.8635 (tpp) cc_final: 0.8270 (tpp) REVERT: D 365 LYS cc_start: 0.9429 (tttt) cc_final: 0.9181 (tttt) REVERT: D 395 LYS cc_start: 0.8318 (mttt) cc_final: 0.8039 (mtmm) REVERT: D 485 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8483 (pp) REVERT: D 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9484 (mmm) outliers start: 8 outliers final: 4 residues processed: 117 average time/residue: 0.1131 time to fit residues: 19.5685 Evaluate side-chains 112 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 148 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.063042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.045475 restraints weight = 65991.582| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.95 r_work: 0.2699 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15124 Z= 0.149 Angle : 0.598 8.804 20613 Z= 0.278 Chirality : 0.039 0.155 2378 Planarity : 0.003 0.043 2543 Dihedral : 10.457 155.794 2103 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.81 % Allowed : 6.58 % Favored : 92.61 % 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: 3.14 (0.20), residues: 1863 helix: 2.92 (0.14), residues: 1296 sheet: 2.86 (0.74), residues: 48 loop : -0.28 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 534 TYR 0.010 0.001 TYR A 511 PHE 0.009 0.001 PHE A 270 TRP 0.006 0.001 TRP B 172 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (15124) covalent geometry : angle 0.59850 / 0.28 (20613) hydrogen bonds : bond 0.03395 / 2.31 ( 970) hydrogen bonds : angle 3.24257 / 2.37 ( 2853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.623 Fit side-chains REVERT: A 100 MET cc_start: 0.9117 (mmp) cc_final: 0.8777 (mmm) REVERT: A 240 MET cc_start: 0.8656 (tpp) cc_final: 0.8255 (tpp) REVERT: A 365 LYS cc_start: 0.9419 (tttt) cc_final: 0.9217 (tttt) REVERT: A 395 LYS cc_start: 0.8403 (mttt) cc_final: 0.8005 (mtmm) REVERT: A 443 LYS cc_start: 0.9605 (mttt) cc_final: 0.9344 (mtmm) REVERT: A 485 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8252 (pp) REVERT: A 494 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9038 (pt) REVERT: A 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9494 (mmm) REVERT: B 100 MET cc_start: 0.9120 (mmp) cc_final: 0.8778 (mmm) REVERT: B 240 MET cc_start: 0.8662 (tpp) cc_final: 0.8258 (tpp) REVERT: B 257 MET cc_start: 0.9373 (tpp) cc_final: 0.9164 (tpp) REVERT: B 365 LYS cc_start: 0.9421 (tttt) cc_final: 0.9218 (tttt) REVERT: B 395 LYS cc_start: 0.8396 (mttt) cc_final: 0.8003 (mtmm) REVERT: B 426 MET cc_start: 0.8510 (mmm) cc_final: 0.8290 (tpp) REVERT: B 443 LYS cc_start: 0.9607 (mttt) cc_final: 0.9328 (mtmm) REVERT: B 485 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8489 (pp) REVERT: B 494 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8957 (pt) REVERT: B 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9488 (mmm) REVERT: C 100 MET cc_start: 0.9118 (mmp) cc_final: 0.8774 (mmm) REVERT: C 240 MET cc_start: 0.8624 (tpp) cc_final: 0.8230 (tpp) REVERT: C 257 MET cc_start: 0.9379 (tpp) cc_final: 0.9171 (tpp) REVERT: C 365 LYS cc_start: 0.9423 (tttt) cc_final: 0.9222 (tttt) REVERT: C 395 LYS cc_start: 0.8400 (mttt) cc_final: 0.8008 (mtmm) REVERT: C 426 MET cc_start: 0.8502 (mmm) cc_final: 0.8290 (tpp) REVERT: C 443 LYS cc_start: 0.9611 (mttt) cc_final: 0.9331 (mtmm) REVERT: C 485 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8490 (pp) REVERT: C 494 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9008 (pt) REVERT: C 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9484 (mmm) REVERT: D 100 MET cc_start: 0.9118 (mmp) cc_final: 0.8778 (mmm) REVERT: D 240 MET cc_start: 0.8623 (tpp) cc_final: 0.8226 (tpp) REVERT: D 365 LYS cc_start: 0.9424 (tttt) cc_final: 0.9222 (tttt) REVERT: D 395 LYS cc_start: 0.8400 (mttt) cc_final: 0.8011 (mtmm) REVERT: D 426 MET cc_start: 0.8503 (mmm) cc_final: 0.8283 (tpp) REVERT: D 443 LYS cc_start: 0.9608 (mttt) cc_final: 0.9325 (mtmm) REVERT: D 485 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8490 (pp) REVERT: D 494 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8961 (pt) REVERT: D 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9486 (mmm) outliers start: 12 outliers final: 4 residues processed: 120 average time/residue: 0.1128 time to fit residues: 20.1626 Evaluate side-chains 117 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 117 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.062523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045067 restraints weight = 65409.392| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.91 r_work: 0.2688 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15124 Z= 0.167 Angle : 0.623 9.176 20613 Z= 0.291 Chirality : 0.040 0.176 2378 Planarity : 0.003 0.043 2543 Dihedral : 10.496 155.515 2103 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.08 % Allowed : 6.58 % Favored : 92.34 % 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: 3.14 (0.20), residues: 1863 helix: 2.91 (0.14), residues: 1296 sheet: 2.76 (0.74), residues: 48 loop : -0.23 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 534 TYR 0.011 0.001 TYR B 95 PHE 0.009 0.001 PHE A 270 TRP 0.008 0.001 TRP D 172 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (15124) covalent geometry : angle 0.62270 / 0.29 (20613) hydrogen bonds : bond 0.03650 / 2.48 ( 970) hydrogen bonds : angle 3.33921 / 2.44 ( 2853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.526 Fit side-chains REVERT: A 100 MET cc_start: 0.9163 (mmp) cc_final: 0.8815 (mmm) REVERT: A 365 LYS cc_start: 0.9433 (tttt) cc_final: 0.9228 (tttt) REVERT: A 395 LYS cc_start: 0.8506 (mttt) cc_final: 0.8092 (mtmm) REVERT: A 443 LYS cc_start: 0.9619 (mttt) cc_final: 0.9336 (mtmm) REVERT: A 485 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8384 (pp) REVERT: A 494 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9086 (pt) REVERT: A 541 MET cc_start: 0.9784 (mmm) cc_final: 0.9503 (mmm) REVERT: B 100 MET cc_start: 0.9167 (mmp) cc_final: 0.8815 (mmm) REVERT: B 257 MET cc_start: 0.9424 (tpp) cc_final: 0.9220 (tpp) REVERT: B 365 LYS cc_start: 0.9434 (tttt) cc_final: 0.9227 (tttt) REVERT: B 395 LYS cc_start: 0.8491 (mttt) cc_final: 0.8084 (mtmm) REVERT: B 426 MET cc_start: 0.8608 (mmm) cc_final: 0.8381 (tpp) REVERT: B 443 LYS cc_start: 0.9621 (mttt) cc_final: 0.9339 (mtmm) REVERT: B 485 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8514 (pp) REVERT: B 494 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9051 (pt) REVERT: B 541 MET cc_start: 0.9770 (mmm) cc_final: 0.9489 (mmm) REVERT: C 100 MET cc_start: 0.9161 (mmp) cc_final: 0.8812 (mmm) REVERT: C 257 MET cc_start: 0.9425 (tpp) cc_final: 0.9222 (tpp) REVERT: C 365 LYS cc_start: 0.9436 (tttt) cc_final: 0.9230 (tttt) REVERT: C 395 LYS cc_start: 0.8491 (mttt) cc_final: 0.8086 (mtmm) REVERT: C 426 MET cc_start: 0.8602 (mmm) cc_final: 0.8381 (tpp) REVERT: C 443 LYS cc_start: 0.9623 (mttt) cc_final: 0.9344 (mtmm) REVERT: C 485 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8519 (pp) REVERT: C 494 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9053 (pt) REVERT: C 541 MET cc_start: 0.9769 (mmm) cc_final: 0.9488 (mmm) REVERT: D 100 MET cc_start: 0.9164 (mmp) cc_final: 0.8816 (mmm) REVERT: D 365 LYS cc_start: 0.9438 (tttt) cc_final: 0.9233 (tttt) REVERT: D 395 LYS cc_start: 0.8493 (mttt) cc_final: 0.8090 (mtmm) REVERT: D 426 MET cc_start: 0.8604 (mmm) cc_final: 0.8374 (tpp) REVERT: D 443 LYS cc_start: 0.9624 (mttt) cc_final: 0.9341 (mtmm) REVERT: D 485 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8513 (pp) REVERT: D 494 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9054 (pt) REVERT: D 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9490 (mmm) outliers start: 16 outliers final: 4 residues processed: 120 average time/residue: 0.1152 time to fit residues: 20.8747 Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.063784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.046309 restraints weight = 65158.471| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.93 r_work: 0.2727 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15124 Z= 0.107 Angle : 0.588 9.834 20613 Z= 0.269 Chirality : 0.038 0.145 2378 Planarity : 0.003 0.044 2543 Dihedral : 10.451 155.697 2103 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.81 % Allowed : 7.12 % Favored : 92.07 % 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: 3.19 (0.20), residues: 1863 helix: 2.92 (0.14), residues: 1296 sheet: 2.18 (0.66), residues: 60 loop : -0.14 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 534 TYR 0.008 0.001 TYR B 95 PHE 0.009 0.001 PHE A 270 TRP 0.012 0.001 TRP C 264 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15124) covalent geometry : angle 0.58814 / 0.27 (20613) hydrogen bonds : bond 0.03133 / 2.13 ( 970) hydrogen bonds : angle 3.19471 / 2.34 ( 2853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2971.10 seconds wall clock time: 51 minutes 40.86 seconds (3100.86 seconds total)