Starting phenix.real_space_refine on Sat Aug 23 21:30:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io0_35603/08_2025/8io0_35603_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io0_35603/08_2025/8io0_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_2025/8io0_35603_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io0_35603/08_2025/8io0_35603_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8io0_35603/08_2025/8io0_35603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io0_35603/08_2025/8io0_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14728 Number of models: 1 Model: "" Number of chains: 5 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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.00, per 1000 atoms: 0.20 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 Links applied TRANS " LEU B 476 " - " VAL B 475 " " LEU C 476 " - " VAL C 475 " " LEU D 476 " - " VAL D 475 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 482.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.42 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: 1.99 Time building geometry restraints manager: 1.31 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: 4571 1.34 - 1.46: 3876 1.46 - 1.58: 6490 1.58 - 1.70: 8 1.70 - 1.82: 176 Bond restraints: 15121 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 B 801 " pdb=" O4' CMP B 801 " ideal model delta sigma weight residual 1.454 1.423 0.031 1.50e-02 4.44e+03 4.18e+00 ... (remaining 15116 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 19580 1.93 - 3.85: 832 3.85 - 5.78: 136 5.78 - 7.70: 48 7.70 - 9.63: 8 Bond angle restraints: 20604 Sorted by residual: angle pdb=" C5' CMP B 801 " pdb=" C4' CMP B 801 " pdb=" O4' CMP B 801 " ideal model delta sigma weight residual 109.10 115.71 -6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C5' CMP A 801 " pdb=" C4' CMP A 801 " pdb=" O4' CMP A 801 " ideal model delta sigma weight residual 109.10 115.71 -6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C5' CMP D 801 " pdb=" C4' CMP D 801 " pdb=" O4' CMP D 801 " ideal model delta sigma weight residual 109.10 115.71 -6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C5' CMP C 801 " pdb=" C4' CMP C 801 " pdb=" O4' CMP C 801 " ideal model delta sigma weight residual 109.10 115.71 -6.61 1.50e+00 4.44e-01 1.94e+01 angle pdb=" C1' CMP D 801 " pdb=" O4' CMP D 801 " pdb=" C4' CMP D 801 " ideal model delta sigma weight residual 109.70 105.43 4.27 1.00e+00 1.00e+00 1.83e+01 ... (remaining 20599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 8745 34.79 - 69.58: 16 69.58 - 104.36: 16 104.36 - 139.15: 0 139.15 - 173.94: 12 Dihedral angle restraints: 8789 sinusoidal: 3236 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 8786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1722 0.054 - 0.108: 528 0.108 - 0.162: 112 0.162 - 0.215: 12 0.215 - 0.269: 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 2.44 2.17 0.27 2.00e-01 2.50e+01 1.81e+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 2.44 2.17 0.27 2.00e-01 2.50e+01 1.81e+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 2.44 2.17 0.27 2.00e-01 2.50e+01 1.81e+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: 0.430 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.620 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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= 0.372 Angle : 0.965 9.629 20613 Z= 0.547 Chirality : 0.053 0.269 2378 Planarity : 0.007 0.062 2540 Dihedral : 12.294 173.940 5182 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 aren 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 covalent geometry : bond 0.00845 (15121) covalent geometry : angle 0.96405 (20604) hydrogen bonds : bond 0.15747 ( 970) hydrogen bonds : angle 5.81752 ( 2853) link_TRANS : bond 0.00188 ( 3) link_TRANS : angle 2.35422 ( 9) *********************** 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 : 0.512 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: 0.8910 (mmm) cc_final: 0.8277 (tpp) REVERT: C 257 MET cc_start: 0.9141 (tpp) cc_final: 0.8838 (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: 0.1378 time to fit residues: 34.8312 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 : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3419 r_free = 0.3419 target = 0.063793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046144 restraints weight = 64435.041| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.90 r_work: 0.2733 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1898 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= 0.149 Angle : 0.590 7.310 20613 Z= 0.312 Chirality : 0.039 0.141 2378 Planarity : 0.004 0.048 2540 Dihedral : 13.260 174.389 2100 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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 aren not related in a simple way. whole: 0.57 (0.19), residues: 1863 helix: 1.13 (0.14), residues: 1292 sheet: 1.12 (0.59), residues: 48 loop : -1.57 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 463 TYR 0.011 0.001 TYR A 95 PHE 0.011 0.001 PHE D 270 TRP 0.016 0.001 TRP A 264 HIS 0.005 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00314 (15121) covalent geometry : angle 0.58974 (20604) hydrogen bonds : bond 0.04443 ( 970) hydrogen bonds : angle 3.87463 ( 2853) link_TRANS : bond 0.00048 ( 3) link_TRANS : angle 0.64308 ( 9) *********************** 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 123 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.445 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: 0.9167 (mmm) cc_final: 0.8669 (tpp) REVERT: A 257 MET cc_start: 0.9434 (tpp) cc_final: 0.9229 (tpp) REVERT: A 395 LYS cc_start: 0.8140 (mttt) cc_final: 0.7441 (mtpt) REVERT: A 465 MET cc_start: 0.9446 (ttm) cc_final: 0.9139 (ttt) REVERT: A 485 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8148 (pt) REVERT: A 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9504 (mmm) REVERT: B 100 MET cc_start: 0.9173 (mmm) cc_final: 0.8682 (tpp) REVERT: B 257 MET cc_start: 0.9422 (tpp) cc_final: 0.9213 (tpp) REVERT: B 395 LYS cc_start: 0.8126 (mttt) cc_final: 0.7434 (mtpt) REVERT: B 465 MET cc_start: 0.9438 (ttm) cc_final: 0.9124 (ttt) REVERT: B 485 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8259 (pt) REVERT: B 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9494 (mmm) REVERT: C 100 MET cc_start: 0.9158 (mmm) cc_final: 0.8662 (tpp) REVERT: C 257 MET cc_start: 0.9433 (tpp) cc_final: 0.9226 (tpp) REVERT: C 395 LYS cc_start: 0.8139 (mttt) cc_final: 0.7446 (mtpt) REVERT: C 465 MET cc_start: 0.9442 (ttm) cc_final: 0.9132 (ttt) REVERT: C 485 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8257 (pt) REVERT: C 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9493 (mmm) REVERT: D 100 MET cc_start: 0.9157 (mmm) cc_final: 0.8667 (tpp) REVERT: D 257 MET cc_start: 0.9431 (tpp) cc_final: 0.9224 (tpp) REVERT: D 395 LYS cc_start: 0.8135 (mttt) cc_final: 0.7443 (mtpt) REVERT: D 465 MET cc_start: 0.9443 (ttm) cc_final: 0.9131 (ttt) REVERT: D 485 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8260 (pt) REVERT: D 541 MET cc_start: 0.9765 (mmm) cc_final: 0.9481 (mmm) outliers start: 4 outliers final: 0 residues processed: 123 average time/residue: 0.1069 time to fit residues: 19.3611 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 : 0.462 ------------------------------------------------------------------------------- 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: 6.9990 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 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: 3.9990 chunk 155 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.064740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.047167 restraints weight = 65286.162| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.99 r_work: 0.2756 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15124 Z= 0.127 Angle : 0.533 7.380 20613 Z= 0.277 Chirality : 0.038 0.115 2378 Planarity : 0.004 0.048 2540 Dihedral : 12.816 170.347 2100 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.54 % Allowed : 5.97 % 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 aren not related in a simple way. whole: 1.87 (0.20), residues: 1863 helix: 2.11 (0.14), residues: 1296 sheet: 1.86 (0.60), residues: 48 loop : -1.11 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 463 TYR 0.009 0.001 TYR D 511 PHE 0.010 0.001 PHE D 270 TRP 0.014 0.001 TRP C 264 HIS 0.004 0.001 HIS D 308 Details of bonding type rmsd covalent geometry : bond 0.00270 (15121) covalent geometry : angle 0.53352 (20604) hydrogen bonds : bond 0.03435 ( 970) hydrogen bonds : angle 3.39544 ( 2853) link_TRANS : bond 0.00045 ( 3) link_TRANS : angle 0.05131 ( 9) *********************** 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 121 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.488 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 257 MET cc_start: 0.9390 (tpp) cc_final: 0.9182 (tpp) REVERT: A 365 LYS cc_start: 0.9414 (tttt) cc_final: 0.9159 (tttt) REVERT: A 426 MET cc_start: 0.8407 (mmm) cc_final: 0.8112 (tpp) REVERT: A 485 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8113 (pp) REVERT: A 531 MET cc_start: 0.9083 (pmm) cc_final: 0.8619 (pmm) REVERT: A 541 MET cc_start: 0.9785 (mmm) cc_final: 0.9516 (mmm) REVERT: B 257 MET cc_start: 0.9373 (tpp) cc_final: 0.9161 (tpp) REVERT: B 365 LYS cc_start: 0.9416 (tttt) cc_final: 0.9160 (tttt) REVERT: B 426 MET cc_start: 0.8408 (mmm) cc_final: 0.8113 (tpp) REVERT: B 485 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8319 (pp) REVERT: B 531 MET cc_start: 0.9084 (pmm) cc_final: 0.8616 (pmm) REVERT: B 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9509 (mmm) REVERT: C 257 MET cc_start: 0.9377 (tpp) cc_final: 0.9164 (tpp) REVERT: C 365 LYS cc_start: 0.9417 (tttt) cc_final: 0.9162 (tttt) REVERT: C 426 MET cc_start: 0.8410 (mmm) cc_final: 0.8116 (tpp) REVERT: C 485 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8318 (pp) REVERT: C 531 MET cc_start: 0.9093 (pmm) cc_final: 0.8630 (pmm) REVERT: C 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9506 (mmm) REVERT: D 257 MET cc_start: 0.9388 (tpp) cc_final: 0.9178 (tpp) REVERT: D 365 LYS cc_start: 0.9417 (tttt) cc_final: 0.9159 (tttt) REVERT: D 426 MET cc_start: 0.8411 (mmm) cc_final: 0.8117 (tpp) REVERT: D 485 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8315 (pp) REVERT: D 531 MET cc_start: 0.9098 (pmm) cc_final: 0.8635 (pmm) REVERT: D 541 MET cc_start: 0.9778 (mmm) cc_final: 0.9502 (mmm) outliers start: 8 outliers final: 4 residues processed: 117 average time/residue: 0.1230 time to fit residues: 21.0118 Evaluate side-chains 116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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: 4.9990 chunk 11 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.044788 restraints weight = 66083.882| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.92 r_work: 0.2685 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15124 Z= 0.217 Angle : 0.600 7.772 20613 Z= 0.315 Chirality : 0.040 0.117 2378 Planarity : 0.004 0.040 2540 Dihedral : 12.705 169.775 2100 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.15 % Allowed : 4.54 % 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 aren not related in a simple way. whole: 2.28 (0.20), residues: 1863 helix: 2.39 (0.14), residues: 1296 sheet: 1.99 (0.62), residues: 48 loop : -0.89 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 507 TYR 0.013 0.002 TYR C 511 PHE 0.013 0.001 PHE A 270 TRP 0.009 0.001 TRP C 264 HIS 0.005 0.001 HIS D 390 Details of bonding type rmsd covalent geometry : bond 0.00483 (15121) covalent geometry : angle 0.60037 (20604) hydrogen bonds : bond 0.04166 ( 970) hydrogen bonds : angle 3.57025 ( 2853) link_TRANS : bond 0.00148 ( 3) link_TRANS : angle 0.28076 ( 9) *********************** 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 125 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9118 (mmm) cc_final: 0.8754 (tpp) REVERT: A 309 MET cc_start: 0.9398 (mtm) cc_final: 0.9168 (mtm) REVERT: A 395 LYS cc_start: 0.8444 (mttt) cc_final: 0.8006 (mtmm) REVERT: A 443 LYS cc_start: 0.9635 (mttt) cc_final: 0.9408 (mtmm) REVERT: A 485 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8192 (pp) REVERT: A 494 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9119 (pt) REVERT: A 531 MET cc_start: 0.9090 (pmm) cc_final: 0.8711 (pmm) REVERT: A 541 MET cc_start: 0.9783 (mmm) cc_final: 0.9523 (mmm) REVERT: B 100 MET cc_start: 0.9125 (mmm) cc_final: 0.8762 (tpp) REVERT: B 309 MET cc_start: 0.9390 (mtm) cc_final: 0.9159 (mtm) REVERT: B 395 LYS cc_start: 0.8445 (mttt) cc_final: 0.8008 (mtmm) REVERT: B 443 LYS cc_start: 0.9637 (mttt) cc_final: 0.9410 (mtmm) REVERT: B 485 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8403 (pp) REVERT: B 531 MET cc_start: 0.9095 (pmm) cc_final: 0.8714 (pmm) REVERT: B 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9518 (mmm) REVERT: C 100 MET cc_start: 0.9115 (mmm) cc_final: 0.8745 (tpp) REVERT: C 309 MET cc_start: 0.9388 (mtm) cc_final: 0.9155 (mtm) REVERT: C 395 LYS cc_start: 0.8445 (mttt) cc_final: 0.8011 (mtmm) REVERT: C 443 LYS cc_start: 0.9636 (mttt) cc_final: 0.9409 (mtmm) REVERT: C 485 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8405 (pp) REVERT: C 531 MET cc_start: 0.9109 (pmm) cc_final: 0.8731 (pmm) REVERT: C 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9514 (mmm) REVERT: D 100 MET cc_start: 0.9117 (mmm) cc_final: 0.8757 (tpp) REVERT: D 309 MET cc_start: 0.9395 (mtm) cc_final: 0.9163 (mtm) REVERT: D 395 LYS cc_start: 0.8450 (mttt) cc_final: 0.8014 (mtmm) REVERT: D 443 LYS cc_start: 0.9639 (mttt) cc_final: 0.9406 (mtmm) REVERT: D 485 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8403 (pp) REVERT: D 531 MET cc_start: 0.9106 (pmm) cc_final: 0.8727 (pmm) REVERT: D 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9520 (mmm) outliers start: 17 outliers final: 4 residues processed: 121 average time/residue: 0.1255 time to fit residues: 21.8117 Evaluate side-chains 113 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 9.9990 chunk 49 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.063342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045749 restraints weight = 64583.317| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.90 r_work: 0.2715 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15124 Z= 0.144 Angle : 0.538 7.483 20613 Z= 0.280 Chirality : 0.038 0.116 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.637 169.403 2100 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.02 % Allowed : 4.68 % 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 aren not related in a simple way. whole: 2.60 (0.20), residues: 1863 helix: 2.60 (0.15), residues: 1296 sheet: 2.28 (0.65), residues: 48 loop : -0.70 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 420 TYR 0.010 0.001 TYR A 95 PHE 0.010 0.001 PHE A 270 TRP 0.014 0.001 TRP A 264 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00312 (15121) covalent geometry : angle 0.53773 (20604) hydrogen bonds : bond 0.03518 ( 970) hydrogen bonds : angle 3.37806 ( 2853) link_TRANS : bond 0.00073 ( 3) link_TRANS : angle 0.13123 ( 9) *********************** 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: 15 poor density : 113 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9069 (mmm) cc_final: 0.8681 (tpp) REVERT: A 309 MET cc_start: 0.9450 (mtm) cc_final: 0.9194 (mtm) REVERT: A 395 LYS cc_start: 0.8425 (mttt) cc_final: 0.7996 (mtmm) REVERT: A 443 LYS cc_start: 0.9604 (mttt) cc_final: 0.9354 (mtmm) REVERT: A 485 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8243 (pp) REVERT: A 531 MET cc_start: 0.9082 (pmm) cc_final: 0.8768 (pmm) REVERT: A 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9505 (mmm) REVERT: B 100 MET cc_start: 0.9078 (mmm) cc_final: 0.8691 (tpp) REVERT: B 309 MET cc_start: 0.9446 (mtm) cc_final: 0.9189 (mtm) REVERT: B 395 LYS cc_start: 0.8423 (mttt) cc_final: 0.7998 (mtmm) REVERT: B 443 LYS cc_start: 0.9602 (mttt) cc_final: 0.9355 (mtmm) REVERT: B 485 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8465 (pp) REVERT: B 494 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.9034 (pt) REVERT: B 531 MET cc_start: 0.9087 (pmm) cc_final: 0.8772 (pmm) REVERT: B 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9503 (mmm) REVERT: C 100 MET cc_start: 0.9066 (mmm) cc_final: 0.8678 (tpp) REVERT: C 309 MET cc_start: 0.9437 (mtm) cc_final: 0.9178 (mtm) REVERT: C 395 LYS cc_start: 0.8419 (mttt) cc_final: 0.7995 (mtmm) REVERT: C 443 LYS cc_start: 0.9606 (mttt) cc_final: 0.9357 (mtmm) REVERT: C 485 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8468 (pp) REVERT: C 494 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9037 (pt) REVERT: C 531 MET cc_start: 0.9097 (pmm) cc_final: 0.8782 (pmm) REVERT: C 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9498 (mmm) REVERT: D 100 MET cc_start: 0.9068 (mmm) cc_final: 0.8685 (tpp) REVERT: D 309 MET cc_start: 0.9444 (mtm) cc_final: 0.9185 (mtm) REVERT: D 395 LYS cc_start: 0.8424 (mttt) cc_final: 0.8003 (mtmm) REVERT: D 443 LYS cc_start: 0.9603 (mttt) cc_final: 0.9351 (mtmm) REVERT: D 485 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8468 (pp) REVERT: D 494 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9038 (pt) REVERT: D 531 MET cc_start: 0.9092 (pmm) cc_final: 0.8778 (pmm) REVERT: D 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9502 (mmm) outliers start: 15 outliers final: 8 residues processed: 124 average time/residue: 0.1105 time to fit residues: 20.7119 Evaluate side-chains 115 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 8 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 156 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.064040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046554 restraints weight = 65034.356| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.87 r_work: 0.2734 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15124 Z= 0.122 Angle : 0.531 7.463 20613 Z= 0.272 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.597 168.977 2100 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.75 % Allowed : 5.56 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.20), residues: 1863 helix: 2.70 (0.14), residues: 1296 sheet: 2.65 (0.71), residues: 48 loop : -0.60 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 420 TYR 0.008 0.001 TYR B 95 PHE 0.010 0.001 PHE C 270 TRP 0.013 0.001 TRP C 264 HIS 0.003 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00260 (15121) covalent geometry : angle 0.53149 (20604) hydrogen bonds : bond 0.03247 ( 970) hydrogen bonds : angle 3.27261 ( 2853) link_TRANS : bond 0.00020 ( 3) link_TRANS : angle 0.11214 ( 9) *********************** 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 117 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.607 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: 0.9061 (mmm) cc_final: 0.8649 (tpp) REVERT: A 240 MET cc_start: 0.8417 (tpp) cc_final: 0.8013 (tpp) REVERT: A 309 MET cc_start: 0.9434 (mtm) cc_final: 0.9189 (mtm) REVERT: A 395 LYS cc_start: 0.8408 (mttt) cc_final: 0.7996 (mtmm) REVERT: A 465 MET cc_start: 0.9066 (ttt) cc_final: 0.8839 (ttp) REVERT: A 485 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8168 (pp) REVERT: A 531 MET cc_start: 0.9073 (pmm) cc_final: 0.8796 (pmm) REVERT: A 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9490 (mmm) REVERT: B 100 MET cc_start: 0.9072 (mmm) cc_final: 0.8664 (tpp) REVERT: B 240 MET cc_start: 0.8424 (tpp) cc_final: 0.8023 (tpp) REVERT: B 309 MET cc_start: 0.9432 (mtm) cc_final: 0.9186 (mtm) REVERT: B 395 LYS cc_start: 0.8403 (mttt) cc_final: 0.7994 (mtmm) REVERT: B 465 MET cc_start: 0.9056 (ttt) cc_final: 0.8823 (ttp) REVERT: B 485 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8445 (pp) REVERT: B 494 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8895 (pt) REVERT: B 531 MET cc_start: 0.9121 (pmm) cc_final: 0.8881 (pmm) REVERT: B 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9492 (mmm) REVERT: C 100 MET cc_start: 0.9054 (mmm) cc_final: 0.8638 (tpp) REVERT: C 240 MET cc_start: 0.8412 (tpp) cc_final: 0.8002 (tpp) REVERT: C 309 MET cc_start: 0.9420 (mtm) cc_final: 0.9171 (mtm) REVERT: C 395 LYS cc_start: 0.8400 (mttt) cc_final: 0.7991 (mtmm) REVERT: C 465 MET cc_start: 0.9070 (ttt) cc_final: 0.8846 (ttp) REVERT: C 485 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8447 (pp) REVERT: C 494 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8899 (pt) REVERT: C 531 MET cc_start: 0.9121 (pmm) cc_final: 0.8882 (pmm) REVERT: C 541 MET cc_start: 0.9767 (mmm) cc_final: 0.9485 (mmm) REVERT: D 100 MET cc_start: 0.9065 (mmm) cc_final: 0.8661 (tpp) REVERT: D 240 MET cc_start: 0.8411 (tpp) cc_final: 0.8003 (tpp) REVERT: D 309 MET cc_start: 0.9431 (mtm) cc_final: 0.9184 (mtm) REVERT: D 395 LYS cc_start: 0.8403 (mttt) cc_final: 0.7996 (mtmm) REVERT: D 465 MET cc_start: 0.9071 (ttt) cc_final: 0.8845 (ttp) REVERT: D 485 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8442 (pp) REVERT: D 494 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8898 (pt) REVERT: D 531 MET cc_start: 0.9125 (pmm) cc_final: 0.8886 (pmm) REVERT: D 541 MET cc_start: 0.9772 (mmm) cc_final: 0.9493 (mmm) outliers start: 11 outliers final: 4 residues processed: 117 average time/residue: 0.1306 time to fit residues: 22.7194 Evaluate side-chains 113 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 187 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.064543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.047154 restraints weight = 64455.010| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.86 r_work: 0.2749 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15124 Z= 0.115 Angle : 0.519 8.247 20613 Z= 0.264 Chirality : 0.037 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.539 168.389 2100 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.81 % Allowed : 5.76 % Favored : 93.42 % 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 aren not related in a simple way. whole: 2.90 (0.20), residues: 1863 helix: 2.77 (0.14), residues: 1296 sheet: 2.86 (0.73), residues: 48 loop : -0.48 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 420 TYR 0.008 0.001 TYR A 95 PHE 0.009 0.001 PHE B 270 TRP 0.012 0.001 TRP B 264 HIS 0.002 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00241 (15121) covalent geometry : angle 0.51932 (20604) hydrogen bonds : bond 0.03040 ( 970) hydrogen bonds : angle 3.20428 ( 2853) link_TRANS : bond 0.00047 ( 3) link_TRANS : angle 0.09808 ( 9) *********************** 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 119 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9055 (mmm) cc_final: 0.8628 (tpp) REVERT: A 240 MET cc_start: 0.8602 (tpp) cc_final: 0.8227 (tpp) REVERT: A 309 MET cc_start: 0.9427 (mtm) cc_final: 0.9180 (mtm) REVERT: A 395 LYS cc_start: 0.8395 (mttt) cc_final: 0.8085 (mtmm) REVERT: A 465 MET cc_start: 0.9050 (ttt) cc_final: 0.8850 (ttp) REVERT: A 485 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8144 (pp) REVERT: A 494 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8680 (pt) REVERT: A 531 MET cc_start: 0.9126 (pmm) cc_final: 0.8709 (pmm) REVERT: A 541 MET cc_start: 0.9772 (mmm) cc_final: 0.9485 (mmm) REVERT: B 100 MET cc_start: 0.9062 (mmm) cc_final: 0.8637 (tpp) REVERT: B 240 MET cc_start: 0.8601 (tpp) cc_final: 0.8229 (tpp) REVERT: B 309 MET cc_start: 0.9427 (mtm) cc_final: 0.9180 (mtm) REVERT: B 395 LYS cc_start: 0.8393 (mttt) cc_final: 0.8082 (mtmm) REVERT: B 465 MET cc_start: 0.9041 (ttt) cc_final: 0.8838 (ttp) REVERT: B 485 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8441 (pp) REVERT: B 494 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8677 (pt) REVERT: B 541 MET cc_start: 0.9772 (mmm) cc_final: 0.9489 (mmm) REVERT: C 100 MET cc_start: 0.9045 (mmm) cc_final: 0.8615 (tpp) REVERT: C 240 MET cc_start: 0.8591 (tpp) cc_final: 0.8225 (tpp) REVERT: C 309 MET cc_start: 0.9416 (mtm) cc_final: 0.9166 (mtm) REVERT: C 395 LYS cc_start: 0.8392 (mttt) cc_final: 0.8081 (mtmm) REVERT: C 485 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8442 (pp) REVERT: C 494 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8679 (pt) REVERT: C 541 MET cc_start: 0.9765 (mmm) cc_final: 0.9476 (mmm) REVERT: D 100 MET cc_start: 0.9056 (mmm) cc_final: 0.8634 (tpp) REVERT: D 240 MET cc_start: 0.8590 (tpp) cc_final: 0.8227 (tpp) REVERT: D 309 MET cc_start: 0.9425 (mtm) cc_final: 0.9177 (mtm) REVERT: D 395 LYS cc_start: 0.8389 (mttt) cc_final: 0.8082 (mtmm) REVERT: D 485 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8437 (pp) REVERT: D 494 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8677 (pt) REVERT: D 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9490 (mmm) outliers start: 12 outliers final: 4 residues processed: 119 average time/residue: 0.1334 time to fit residues: 23.5506 Evaluate side-chains 114 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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: 0.3980 chunk 86 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 51 optimal weight: 7.9990 chunk 151 optimal weight: 0.0060 chunk 123 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.064651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047132 restraints weight = 65271.245| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.91 r_work: 0.2749 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15124 Z= 0.111 Angle : 0.524 8.564 20613 Z= 0.265 Chirality : 0.037 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.522 168.810 2100 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 6.24 % Favored : 92.68 % 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 aren not related in a simple way. whole: 2.96 (0.20), residues: 1863 helix: 2.81 (0.14), residues: 1296 sheet: 2.88 (0.74), residues: 48 loop : -0.44 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 534 TYR 0.008 0.001 TYR B 364 PHE 0.009 0.001 PHE D 270 TRP 0.012 0.001 TRP C 264 HIS 0.003 0.001 HIS C 308 Details of bonding type rmsd covalent geometry : bond 0.00233 (15121) covalent geometry : angle 0.52431 (20604) hydrogen bonds : bond 0.02972 ( 970) hydrogen bonds : angle 3.16820 ( 2853) link_TRANS : bond 0.00053 ( 3) link_TRANS : angle 0.13945 ( 9) *********************** 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 126 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.620 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: 0.9050 (mmm) cc_final: 0.8620 (tpp) REVERT: A 240 MET cc_start: 0.8615 (tpp) cc_final: 0.8228 (tpp) REVERT: A 309 MET cc_start: 0.9416 (mtm) cc_final: 0.9166 (mtm) REVERT: A 395 LYS cc_start: 0.8400 (mttt) cc_final: 0.8095 (mtmm) REVERT: A 485 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8141 (pp) REVERT: A 494 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8630 (pt) REVERT: A 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9484 (mmm) REVERT: B 100 MET cc_start: 0.9061 (mmm) cc_final: 0.8632 (tpp) REVERT: B 240 MET cc_start: 0.8611 (tpp) cc_final: 0.8221 (tpp) REVERT: B 309 MET cc_start: 0.9424 (mtm) cc_final: 0.9176 (mtm) REVERT: B 395 LYS cc_start: 0.8393 (mttt) cc_final: 0.8090 (mtmm) REVERT: B 485 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8475 (pp) REVERT: B 494 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8633 (pt) REVERT: B 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9483 (mmm) REVERT: C 100 MET cc_start: 0.9045 (mmm) cc_final: 0.8614 (tpp) REVERT: C 240 MET cc_start: 0.8622 (tpp) cc_final: 0.8236 (tpp) REVERT: C 309 MET cc_start: 0.9418 (mtm) cc_final: 0.9169 (mtm) REVERT: C 395 LYS cc_start: 0.8398 (mttt) cc_final: 0.8092 (mtmm) REVERT: C 485 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8480 (pp) REVERT: C 494 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8665 (pt) REVERT: C 541 MET cc_start: 0.9768 (mmm) cc_final: 0.9478 (mmm) REVERT: D 100 MET cc_start: 0.9053 (mmm) cc_final: 0.8628 (tpp) REVERT: D 240 MET cc_start: 0.8617 (tpp) cc_final: 0.8228 (tpp) REVERT: D 309 MET cc_start: 0.9430 (mtm) cc_final: 0.9183 (mtm) REVERT: D 395 LYS cc_start: 0.8394 (mttt) cc_final: 0.8093 (mtmm) REVERT: D 485 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8471 (pp) REVERT: D 494 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8779 (pt) REVERT: D 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9484 (mmm) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.1251 time to fit residues: 22.8037 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 : 0.595 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 148 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.065008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.047493 restraints weight = 64992.871| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.92 r_work: 0.2764 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15124 Z= 0.106 Angle : 0.534 8.972 20613 Z= 0.266 Chirality : 0.037 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.516 168.965 2100 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.02 % Allowed : 6.64 % 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 aren not related in a simple way. whole: 2.96 (0.20), residues: 1863 helix: 2.81 (0.14), residues: 1300 sheet: 2.93 (0.74), residues: 48 loop : -0.45 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 534 TYR 0.009 0.001 TYR B 364 PHE 0.009 0.001 PHE B 270 TRP 0.011 0.001 TRP A 264 HIS 0.002 0.000 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00219 (15121) covalent geometry : angle 0.53458 (20604) hydrogen bonds : bond 0.02842 ( 970) hydrogen bonds : angle 3.13635 ( 2853) link_TRANS : bond 0.00072 ( 3) link_TRANS : angle 0.14870 ( 9) *********************** 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 125 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9038 (mmm) cc_final: 0.8607 (tpp) REVERT: A 240 MET cc_start: 0.8655 (tpp) cc_final: 0.8270 (tpp) REVERT: A 309 MET cc_start: 0.9405 (mtm) cc_final: 0.9164 (mtm) REVERT: A 395 LYS cc_start: 0.8343 (mttt) cc_final: 0.8057 (mtmm) REVERT: A 426 MET cc_start: 0.8384 (mmm) cc_final: 0.8118 (tpp) REVERT: A 485 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8129 (pp) REVERT: A 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9485 (mmm) REVERT: B 100 MET cc_start: 0.9049 (mmm) cc_final: 0.8622 (tpp) REVERT: B 240 MET cc_start: 0.8649 (tpp) cc_final: 0.8260 (tpp) REVERT: B 309 MET cc_start: 0.9406 (mtm) cc_final: 0.9164 (mtm) REVERT: B 395 LYS cc_start: 0.8336 (mttt) cc_final: 0.8051 (mtmm) REVERT: B 426 MET cc_start: 0.8398 (mmm) cc_final: 0.8127 (tpp) REVERT: B 485 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8471 (pp) REVERT: B 494 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8605 (pt) REVERT: B 541 MET cc_start: 0.9769 (mmm) cc_final: 0.9476 (mmm) REVERT: C 100 MET cc_start: 0.9035 (mmm) cc_final: 0.8607 (tpp) REVERT: C 240 MET cc_start: 0.8632 (tpp) cc_final: 0.8268 (tpp) REVERT: C 309 MET cc_start: 0.9402 (mtm) cc_final: 0.9161 (mtm) REVERT: C 395 LYS cc_start: 0.8347 (mttt) cc_final: 0.8059 (mtmm) REVERT: C 426 MET cc_start: 0.8387 (mmm) cc_final: 0.8122 (tpp) REVERT: C 485 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 494 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8620 (pt) REVERT: C 541 MET cc_start: 0.9769 (mmm) cc_final: 0.9475 (mmm) REVERT: D 100 MET cc_start: 0.9042 (mmm) cc_final: 0.8617 (tpp) REVERT: D 240 MET cc_start: 0.8626 (tpp) cc_final: 0.8233 (tpp) REVERT: D 309 MET cc_start: 0.9408 (mtm) cc_final: 0.9166 (mtm) REVERT: D 395 LYS cc_start: 0.8345 (mttt) cc_final: 0.8064 (mtmm) REVERT: D 426 MET cc_start: 0.8388 (mmm) cc_final: 0.8115 (tpp) REVERT: D 485 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8472 (pp) REVERT: D 494 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8621 (pt) REVERT: D 541 MET cc_start: 0.9773 (mmm) cc_final: 0.9482 (mmm) outliers start: 15 outliers final: 4 residues processed: 121 average time/residue: 0.1280 time to fit residues: 23.0326 Evaluate side-chains 121 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 133 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.064637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.047126 restraints weight = 64948.093| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.91 r_work: 0.2754 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15124 Z= 0.114 Angle : 0.546 9.263 20613 Z= 0.271 Chirality : 0.038 0.120 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.493 168.503 2100 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.56 % Allowed : 5.83 % 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 aren not related in a simple way. whole: 2.99 (0.20), residues: 1863 helix: 2.83 (0.14), residues: 1300 sheet: 2.97 (0.74), residues: 48 loop : -0.45 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 534 TYR 0.009 0.001 TYR D 364 PHE 0.009 0.001 PHE D 270 TRP 0.011 0.001 TRP A 264 HIS 0.002 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00242 (15121) covalent geometry : angle 0.54625 (20604) hydrogen bonds : bond 0.02965 ( 970) hydrogen bonds : angle 3.15050 ( 2853) link_TRANS : bond 0.00044 ( 3) link_TRANS : angle 0.13499 ( 9) ********************** 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 131 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9050 (mmm) cc_final: 0.8622 (tpp) REVERT: A 240 MET cc_start: 0.8653 (tpp) cc_final: 0.8278 (tpp) REVERT: A 309 MET cc_start: 0.9414 (mtm) cc_final: 0.9160 (mtm) REVERT: A 395 LYS cc_start: 0.8383 (mttt) cc_final: 0.8087 (mtmm) REVERT: A 485 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8139 (pp) REVERT: A 541 MET cc_start: 0.9775 (mmm) cc_final: 0.9480 (mmm) REVERT: B 100 MET cc_start: 0.9060 (mmm) cc_final: 0.8633 (tpp) REVERT: B 240 MET cc_start: 0.8649 (tpp) cc_final: 0.8270 (tpp) REVERT: B 309 MET cc_start: 0.9415 (mtm) cc_final: 0.9160 (mtm) REVERT: B 395 LYS cc_start: 0.8366 (mttt) cc_final: 0.8074 (mtmm) REVERT: B 485 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8473 (pp) REVERT: B 494 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8630 (pt) REVERT: B 541 MET cc_start: 0.9765 (mmm) cc_final: 0.9465 (mmm) REVERT: C 100 MET cc_start: 0.9048 (mmm) cc_final: 0.8620 (tpp) REVERT: C 240 MET cc_start: 0.8639 (tpp) cc_final: 0.8265 (tpp) REVERT: C 309 MET cc_start: 0.9416 (mtm) cc_final: 0.9161 (mtm) REVERT: C 395 LYS cc_start: 0.8386 (mttt) cc_final: 0.8090 (mtmm) REVERT: C 485 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8420 (pp) REVERT: C 494 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8639 (pt) REVERT: C 541 MET cc_start: 0.9768 (mmm) cc_final: 0.9471 (mmm) REVERT: D 100 MET cc_start: 0.9050 (mmm) cc_final: 0.8626 (tpp) REVERT: D 240 MET cc_start: 0.8639 (tpp) cc_final: 0.8265 (tpp) REVERT: D 309 MET cc_start: 0.9419 (mtm) cc_final: 0.9166 (mtm) REVERT: D 395 LYS cc_start: 0.8378 (mttt) cc_final: 0.8088 (mtmm) REVERT: D 485 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8416 (pp) REVERT: D 494 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8642 (pt) REVERT: D 541 MET cc_start: 0.9770 (mmm) cc_final: 0.9472 (mmm) outliers start: 23 outliers final: 8 residues processed: 123 average time/residue: 0.1204 time to fit residues: 22.1552 Evaluate side-chains 121 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 chunk 125 optimal weight: 10.0000 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.046196 restraints weight = 64669.378| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.87 r_work: 0.2727 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15124 Z= 0.147 Angle : 0.589 9.381 20613 Z= 0.294 Chirality : 0.039 0.163 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.469 168.451 2100 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.29 % Allowed : 6.37 % 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 aren not related in a simple way. whole: 3.04 (0.20), residues: 1863 helix: 2.85 (0.14), residues: 1300 sheet: 2.94 (0.74), residues: 48 loop : -0.35 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 534 TYR 0.009 0.001 TYR A 511 PHE 0.009 0.001 PHE C 270 TRP 0.007 0.001 TRP A 264 HIS 0.003 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00325 (15121) covalent geometry : angle 0.58954 (20604) hydrogen bonds : bond 0.03375 ( 970) hydrogen bonds : angle 3.25959 ( 2853) link_TRANS : bond 0.00012 ( 3) link_TRANS : angle 0.11009 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3088.79 seconds wall clock time: 53 minutes 46.14 seconds (3226.14 seconds total)