Starting phenix.real_space_refine on Fri May 16 20:04:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io0_35603/05_2025/8io0_35603_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io0_35603/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8io0_35603/05_2025/8io0_35603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io0_35603/05_2025/8io0_35603.map" model { file = "/net/cci-nas-00/data/ceres_data/8io0_35603/05_2025/8io0_35603_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io0_35603/05_2025/8io0_35603_neut.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ASP:plan': 7, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} 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: 7.66, per 1000 atoms: 0.52 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: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.55 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: 4.84 Time building geometry restraints manager: 3.47 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 546 or resid 801)) selection = (chain 'C' and (resid 50 through 475 or resid 483 through 546 or resid 801)) selection = (chain 'D' and (resid 50 through 475 or resid 483 through 546 or resid 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: 0.450 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: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 30.790 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.053 0.003 TRP B 234 HIS 0.016 0.003 HIS B 390 PHE 0.048 0.003 PHE D 238 TYR 0.024 0.003 TYR D 511 ARG 0.004 0.001 ARG A 420 Details of bonding type rmsd link_TRANS : bond 0.00188 ( 3) link_TRANS : angle 2.35422 ( 9) hydrogen bonds : bond 0.15747 ( 970) hydrogen bonds : angle 5.81752 ( 2853) covalent geometry : bond 0.00845 (15121) covalent geometry : angle 0.96405 (20604) *********************** 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 : 1.713 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 363 LYS cc_start: 0.9264 (ttpm) cc_final: 0.8835 (ttpt) 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 363 LYS cc_start: 0.9267 (ttpm) cc_final: 0.8837 (ttpt) 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 363 LYS cc_start: 0.9263 (ttpm) cc_final: 0.8833 (ttpt) 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 363 LYS cc_start: 0.9263 (ttpm) cc_final: 0.8834 (ttpt) 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: 0.3647 time to fit residues: 92.5899 Evaluate side-chains 113 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 158 optimal weight: 5.9990 chunk 142 optimal weight: 0.0870 chunk 79 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.0980 chunk 170 optimal weight: 2.9990 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 292 HIS A 308 HIS A 470 HIS A 521 HIS B 107 ASN B 292 HIS B 308 HIS B 470 HIS B 521 HIS C 107 ASN C 292 HIS C 308 HIS C 470 HIS C 521 HIS D 107 ASN D 292 HIS D 308 HIS D 470 HIS D 521 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.065570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048057 restraints weight = 63473.633| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.89 r_work: 0.2786 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15124 Z= 0.117 Angle : 0.562 8.255 20613 Z= 0.293 Chirality : 0.038 0.122 2378 Planarity : 0.004 0.047 2540 Dihedral : 13.228 173.964 2100 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.27 % Allowed : 5.36 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1863 helix: 1.17 (0.14), residues: 1288 sheet: 1.27 (0.59), residues: 48 loop : -1.59 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 264 HIS 0.005 0.001 HIS C 308 PHE 0.010 0.001 PHE D 270 TYR 0.010 0.001 TYR A 364 ARG 0.005 0.000 ARG A 463 Details of bonding type rmsd link_TRANS : bond 0.00067 ( 3) link_TRANS : angle 0.78020 ( 9) hydrogen bonds : bond 0.03782 ( 970) hydrogen bonds : angle 3.76398 ( 2853) covalent geometry : bond 0.00229 (15121) covalent geometry : angle 0.56238 (20604) *********************** 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 132 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9077 (mmm) cc_final: 0.8580 (tpp) REVERT: A 257 MET cc_start: 0.9422 (tpp) cc_final: 0.9216 (tpp) REVERT: A 395 LYS cc_start: 0.7970 (mttt) cc_final: 0.7290 (mtpt) REVERT: A 465 MET cc_start: 0.9423 (ttm) cc_final: 0.9122 (ttt) REVERT: A 485 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8112 (pt) REVERT: A 541 MET cc_start: 0.9784 (mmm) cc_final: 0.9507 (mmm) REVERT: B 100 MET cc_start: 0.9082 (mmm) cc_final: 0.8589 (tpp) REVERT: B 257 MET cc_start: 0.9413 (tpp) cc_final: 0.9204 (tpp) REVERT: B 395 LYS cc_start: 0.7963 (mttt) cc_final: 0.7288 (mtpt) REVERT: B 465 MET cc_start: 0.9414 (ttm) cc_final: 0.9107 (ttt) REVERT: B 485 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8233 (pt) REVERT: B 541 MET cc_start: 0.9775 (mmm) cc_final: 0.9491 (mmm) REVERT: C 100 MET cc_start: 0.9069 (mmm) cc_final: 0.8576 (tpp) REVERT: C 257 MET cc_start: 0.9423 (tpp) cc_final: 0.9214 (tpp) REVERT: C 395 LYS cc_start: 0.7980 (mttt) cc_final: 0.7307 (mtpt) REVERT: C 465 MET cc_start: 0.9415 (ttm) cc_final: 0.9112 (ttt) REVERT: C 485 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8237 (pt) REVERT: C 541 MET cc_start: 0.9775 (mmm) cc_final: 0.9490 (mmm) REVERT: D 100 MET cc_start: 0.9072 (mmm) cc_final: 0.8583 (tpp) REVERT: D 257 MET cc_start: 0.9418 (tpp) cc_final: 0.9209 (tpp) REVERT: D 395 LYS cc_start: 0.7973 (mttt) cc_final: 0.7297 (mtpt) REVERT: D 465 MET cc_start: 0.9421 (ttm) cc_final: 0.9118 (ttt) REVERT: D 485 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8237 (pt) REVERT: D 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9485 (mmm) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.2952 time to fit residues: 56.1502 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 : 1.601 ------------------------------------------------------------------------------- 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 133 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 169 optimal weight: 10.0000 chunk 97 optimal weight: 0.0050 chunk 7 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 overall best weight: 1.7798 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.064886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.047421 restraints weight = 64629.545| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.96 r_work: 0.2772 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2428 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= 0.124 Angle : 0.535 7.406 20613 Z= 0.277 Chirality : 0.037 0.115 2378 Planarity : 0.004 0.045 2540 Dihedral : 12.810 170.258 2100 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.54 % Allowed : 6.51 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 1863 helix: 2.03 (0.14), residues: 1296 sheet: 1.93 (0.61), residues: 48 loop : -1.16 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 264 HIS 0.004 0.001 HIS B 308 PHE 0.011 0.001 PHE A 270 TYR 0.008 0.001 TYR C 511 ARG 0.005 0.000 ARG B 63 Details of bonding type rmsd link_TRANS : bond 0.00009 ( 3) link_TRANS : angle 0.04885 ( 9) hydrogen bonds : bond 0.03441 ( 970) hydrogen bonds : angle 3.36178 ( 2853) covalent geometry : bond 0.00259 (15121) covalent geometry : angle 0.53537 (20604) *********************** 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 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9113 (mmm) cc_final: 0.8562 (tpp) REVERT: A 257 MET cc_start: 0.9395 (tpp) cc_final: 0.9184 (tpp) REVERT: A 365 LYS cc_start: 0.9383 (tttt) cc_final: 0.9178 (tttt) REVERT: A 395 LYS cc_start: 0.8252 (mttt) cc_final: 0.7531 (mtpt) REVERT: A 426 MET cc_start: 0.8464 (mmm) cc_final: 0.8190 (tpp) REVERT: A 485 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8261 (pp) REVERT: A 531 MET cc_start: 0.9053 (pmm) cc_final: 0.8575 (pmm) REVERT: A 541 MET cc_start: 0.9788 (mmm) cc_final: 0.9517 (mmm) REVERT: B 100 MET cc_start: 0.9122 (mmm) cc_final: 0.8577 (tpp) REVERT: B 257 MET cc_start: 0.9386 (tpp) cc_final: 0.9172 (tpp) REVERT: B 365 LYS cc_start: 0.9384 (tttt) cc_final: 0.9177 (tttt) REVERT: B 395 LYS cc_start: 0.8243 (mttt) cc_final: 0.7531 (mtpt) REVERT: B 426 MET cc_start: 0.8463 (mmm) cc_final: 0.8186 (tpp) REVERT: B 485 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8351 (pp) REVERT: B 531 MET cc_start: 0.9054 (pmm) cc_final: 0.8576 (pmm) REVERT: B 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9509 (mmm) REVERT: C 100 MET cc_start: 0.9110 (mmm) cc_final: 0.8557 (tpp) REVERT: C 257 MET cc_start: 0.9387 (tpp) cc_final: 0.9171 (tpp) REVERT: C 365 LYS cc_start: 0.9389 (tttt) cc_final: 0.9184 (tttt) REVERT: C 395 LYS cc_start: 0.8243 (mttt) cc_final: 0.7532 (mtpt) REVERT: C 426 MET cc_start: 0.8465 (mmm) cc_final: 0.8191 (tpp) REVERT: C 485 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8350 (pp) REVERT: C 531 MET cc_start: 0.9072 (pmm) cc_final: 0.8597 (pmm) REVERT: C 541 MET cc_start: 0.9783 (mmm) cc_final: 0.9512 (mmm) REVERT: D 100 MET cc_start: 0.9115 (mmm) cc_final: 0.8571 (tpp) REVERT: D 257 MET cc_start: 0.9394 (tpp) cc_final: 0.9180 (tpp) REVERT: D 365 LYS cc_start: 0.9385 (tttt) cc_final: 0.9177 (tttt) REVERT: D 395 LYS cc_start: 0.8243 (mttt) cc_final: 0.7529 (mtpt) REVERT: D 426 MET cc_start: 0.8461 (mmm) cc_final: 0.8186 (tpp) REVERT: D 485 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8349 (pp) REVERT: D 531 MET cc_start: 0.9066 (pmm) cc_final: 0.8592 (pmm) REVERT: D 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9508 (mmm) outliers start: 8 outliers final: 4 residues processed: 116 average time/residue: 0.2910 time to fit residues: 49.1826 Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 35 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 162 optimal weight: 0.0040 chunk 47 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.064480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046866 restraints weight = 64197.611| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.91 r_work: 0.2753 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2640 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= 0.128 Angle : 0.518 7.515 20613 Z= 0.269 Chirality : 0.037 0.117 2378 Planarity : 0.003 0.041 2540 Dihedral : 12.637 168.594 2100 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.36 % Allowed : 5.56 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.20), residues: 1863 helix: 2.46 (0.15), residues: 1296 sheet: 1.97 (0.61), residues: 48 loop : -0.93 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 264 HIS 0.003 0.001 HIS C 390 PHE 0.010 0.001 PHE D 270 TYR 0.008 0.001 TYR B 511 ARG 0.002 0.000 ARG D 507 Details of bonding type rmsd link_TRANS : bond 0.00034 ( 3) link_TRANS : angle 0.16802 ( 9) hydrogen bonds : bond 0.03311 ( 970) hydrogen bonds : angle 3.28711 ( 2853) covalent geometry : bond 0.00277 (15121) covalent geometry : angle 0.51810 (20604) *********************** 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 136 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.601 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: 0.9145 (mmm) cc_final: 0.8921 (mmm) REVERT: A 426 MET cc_start: 0.8360 (mmm) cc_final: 0.8102 (tpp) REVERT: A 485 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8110 (pp) REVERT: A 531 MET cc_start: 0.9071 (pmm) cc_final: 0.8688 (pmm) REVERT: A 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9508 (mmm) REVERT: B 100 MET cc_start: 0.9154 (mmm) cc_final: 0.8928 (mmm) REVERT: B 426 MET cc_start: 0.8363 (mmm) cc_final: 0.8105 (tpp) REVERT: B 485 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8401 (pp) REVERT: B 531 MET cc_start: 0.9075 (pmm) cc_final: 0.8691 (pmm) REVERT: B 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9511 (mmm) REVERT: C 100 MET cc_start: 0.9147 (mmm) cc_final: 0.8920 (mmm) REVERT: C 426 MET cc_start: 0.8361 (mmm) cc_final: 0.8101 (tpp) REVERT: C 485 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8403 (pp) REVERT: C 531 MET cc_start: 0.9082 (pmm) cc_final: 0.8700 (pmm) REVERT: C 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9512 (mmm) REVERT: D 100 MET cc_start: 0.9150 (mmm) cc_final: 0.8926 (mmm) REVERT: D 426 MET cc_start: 0.8361 (mmm) cc_final: 0.8105 (tpp) REVERT: D 485 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8407 (pp) REVERT: D 531 MET cc_start: 0.9087 (pmm) cc_final: 0.8706 (pmm) REVERT: D 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9516 (mmm) outliers start: 20 outliers final: 4 residues processed: 128 average time/residue: 0.3032 time to fit residues: 54.9835 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 : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 234 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 124 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.063733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046198 restraints weight = 65443.576| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.91 r_work: 0.2732 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2851 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 : 0.535 7.560 20613 Z= 0.278 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.547 168.135 2100 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.81 % Allowed : 5.56 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.20), residues: 1863 helix: 2.66 (0.15), residues: 1296 sheet: 2.28 (0.66), residues: 48 loop : -0.75 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 264 HIS 0.003 0.001 HIS D 390 PHE 0.010 0.001 PHE D 270 TYR 0.010 0.001 TYR D 511 ARG 0.003 0.000 ARG B 420 Details of bonding type rmsd link_TRANS : bond 0.00054 ( 3) link_TRANS : angle 0.15094 ( 9) hydrogen bonds : bond 0.03515 ( 970) hydrogen bonds : angle 3.30667 ( 2853) covalent geometry : bond 0.00322 (15121) covalent geometry : angle 0.53493 (20604) *********************** 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 131 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.543 Fit side-chains REVERT: A 100 MET cc_start: 0.9195 (mmm) cc_final: 0.8910 (mmm) REVERT: A 365 LYS cc_start: 0.9415 (tttt) cc_final: 0.9196 (tttt) REVERT: A 395 LYS cc_start: 0.8371 (mttt) cc_final: 0.7940 (mtmm) REVERT: A 426 MET cc_start: 0.8488 (mmm) cc_final: 0.8114 (tpp) REVERT: A 443 LYS cc_start: 0.9608 (mttt) cc_final: 0.9345 (mtmm) REVERT: A 485 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8213 (pp) REVERT: A 531 MET cc_start: 0.9117 (pmm) cc_final: 0.8766 (pmm) REVERT: A 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9505 (mmm) REVERT: B 100 MET cc_start: 0.9202 (mmm) cc_final: 0.8915 (mmm) REVERT: B 365 LYS cc_start: 0.9415 (tttt) cc_final: 0.9194 (tttt) REVERT: B 395 LYS cc_start: 0.8374 (mttt) cc_final: 0.7947 (mtmm) REVERT: B 426 MET cc_start: 0.8493 (mmm) cc_final: 0.8121 (tpp) REVERT: B 443 LYS cc_start: 0.9609 (mttt) cc_final: 0.9348 (mtmm) REVERT: B 485 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8479 (pp) REVERT: B 531 MET cc_start: 0.9116 (pmm) cc_final: 0.8764 (pmm) REVERT: B 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9501 (mmm) REVERT: C 100 MET cc_start: 0.9191 (mmm) cc_final: 0.8902 (mmm) REVERT: C 365 LYS cc_start: 0.9417 (tttt) cc_final: 0.9196 (tttt) REVERT: C 395 LYS cc_start: 0.8377 (mttt) cc_final: 0.7948 (mtmm) REVERT: C 426 MET cc_start: 0.8489 (mmm) cc_final: 0.8116 (tpp) REVERT: C 443 LYS cc_start: 0.9614 (mttt) cc_final: 0.9352 (mtmm) REVERT: C 485 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8479 (pp) REVERT: C 531 MET cc_start: 0.9125 (pmm) cc_final: 0.8776 (pmm) REVERT: C 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9506 (mmm) REVERT: D 100 MET cc_start: 0.9200 (mmm) cc_final: 0.8913 (mmm) REVERT: D 365 LYS cc_start: 0.9419 (tttt) cc_final: 0.9200 (tttt) REVERT: D 395 LYS cc_start: 0.8380 (mttt) cc_final: 0.7956 (mtmm) REVERT: D 426 MET cc_start: 0.8493 (mmm) cc_final: 0.8124 (tpp) REVERT: D 443 LYS cc_start: 0.9613 (mttt) cc_final: 0.9347 (mtmm) REVERT: D 485 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8481 (pp) REVERT: D 531 MET cc_start: 0.9122 (pmm) cc_final: 0.8773 (pmm) REVERT: D 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9507 (mmm) outliers start: 12 outliers final: 4 residues processed: 123 average time/residue: 0.2833 time to fit residues: 51.0629 Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 234 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.063894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.046373 restraints weight = 65055.781| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.90 r_work: 0.2733 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2985 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= 0.146 Angle : 0.542 7.676 20613 Z= 0.277 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.528 168.296 2100 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.08 % Allowed : 5.90 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.20), residues: 1863 helix: 2.73 (0.14), residues: 1296 sheet: 2.64 (0.71), residues: 48 loop : -0.66 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 264 HIS 0.003 0.001 HIS C 390 PHE 0.010 0.001 PHE C 270 TYR 0.009 0.001 TYR A 95 ARG 0.002 0.000 ARG A 420 Details of bonding type rmsd link_TRANS : bond 0.00146 ( 3) link_TRANS : angle 0.19945 ( 9) hydrogen bonds : bond 0.03406 ( 970) hydrogen bonds : angle 3.28141 ( 2853) covalent geometry : bond 0.00319 (15121) covalent geometry : angle 0.54167 (20604) *********************** 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 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.758 Fit side-chains REVERT: A 100 MET cc_start: 0.9183 (mmm) cc_final: 0.8857 (mmm) REVERT: A 395 LYS cc_start: 0.8385 (mttt) cc_final: 0.7958 (mtmm) REVERT: A 426 MET cc_start: 0.8369 (mmm) cc_final: 0.8144 (tpp) REVERT: A 443 LYS cc_start: 0.9604 (mttt) cc_final: 0.9322 (mtmm) REVERT: A 485 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8153 (pp) REVERT: A 494 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8767 (pt) REVERT: A 531 MET cc_start: 0.9070 (pmm) cc_final: 0.8786 (pmm) REVERT: A 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9504 (mmm) REVERT: B 100 MET cc_start: 0.9189 (mmm) cc_final: 0.8864 (mmm) REVERT: B 395 LYS cc_start: 0.8388 (mttt) cc_final: 0.7962 (mtmm) REVERT: B 426 MET cc_start: 0.8376 (mmm) cc_final: 0.8150 (tpp) REVERT: B 485 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 494 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8760 (pt) REVERT: B 531 MET cc_start: 0.9081 (pmm) cc_final: 0.8798 (pmm) REVERT: B 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9503 (mmm) REVERT: C 100 MET cc_start: 0.9181 (mmm) cc_final: 0.8850 (mmm) REVERT: C 395 LYS cc_start: 0.8387 (mttt) cc_final: 0.7961 (mtmm) REVERT: C 426 MET cc_start: 0.8370 (mmm) cc_final: 0.8147 (tpp) REVERT: C 485 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8543 (pp) REVERT: C 494 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8766 (pt) REVERT: C 531 MET cc_start: 0.9083 (pmm) cc_final: 0.8800 (pmm) REVERT: C 541 MET cc_start: 0.9778 (mmm) cc_final: 0.9498 (mmm) REVERT: D 100 MET cc_start: 0.9184 (mmm) cc_final: 0.8855 (mmm) REVERT: D 395 LYS cc_start: 0.8385 (mttt) cc_final: 0.7967 (mtmm) REVERT: D 426 MET cc_start: 0.8371 (mmm) cc_final: 0.8150 (tpp) REVERT: D 485 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8544 (pp) REVERT: D 494 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8766 (pt) REVERT: D 531 MET cc_start: 0.9083 (pmm) cc_final: 0.8800 (pmm) REVERT: D 541 MET cc_start: 0.9783 (mmm) cc_final: 0.9507 (mmm) outliers start: 16 outliers final: 4 residues processed: 120 average time/residue: 0.3062 time to fit residues: 53.5446 Evaluate side-chains 113 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 144 optimal weight: 0.1980 chunk 175 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS B 300 HIS C 300 HIS D 300 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.046393 restraints weight = 65860.061| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.94 r_work: 0.2732 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15124 Z= 0.142 Angle : 0.535 8.089 20613 Z= 0.275 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.503 168.809 2100 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.81 % Allowed : 5.90 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.20), residues: 1863 helix: 2.80 (0.14), residues: 1296 sheet: 2.79 (0.74), residues: 48 loop : -0.61 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.006 0.001 HIS D 300 PHE 0.009 0.001 PHE C 270 TYR 0.010 0.001 TYR C 95 ARG 0.003 0.000 ARG C 420 Details of bonding type rmsd link_TRANS : bond 0.00051 ( 3) link_TRANS : angle 0.13421 ( 9) hydrogen bonds : bond 0.03372 ( 970) hydrogen bonds : angle 3.27268 ( 2853) covalent geometry : bond 0.00308 (15121) covalent geometry : angle 0.53524 (20604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.796 Fit side-chains REVERT: A 100 MET cc_start: 0.9199 (mmm) cc_final: 0.8871 (mmm) REVERT: A 395 LYS cc_start: 0.8364 (mttt) cc_final: 0.7961 (mtmm) REVERT: A 485 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8171 (pp) REVERT: A 531 MET cc_start: 0.9074 (pmm) cc_final: 0.8841 (pmm) REVERT: A 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9495 (mmm) REVERT: B 100 MET cc_start: 0.9206 (mmm) cc_final: 0.8875 (mmm) REVERT: B 395 LYS cc_start: 0.8363 (mttt) cc_final: 0.7962 (mtmm) REVERT: B 485 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8547 (pp) REVERT: B 531 MET cc_start: 0.9086 (pmm) cc_final: 0.8854 (pmm) REVERT: B 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9494 (mmm) REVERT: C 100 MET cc_start: 0.9196 (mmm) cc_final: 0.8860 (mmm) REVERT: C 395 LYS cc_start: 0.8368 (mttt) cc_final: 0.7968 (mtmm) REVERT: C 485 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8546 (pp) REVERT: C 531 MET cc_start: 0.9083 (pmm) cc_final: 0.8852 (pmm) REVERT: C 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9488 (mmm) REVERT: D 100 MET cc_start: 0.9204 (mmm) cc_final: 0.8870 (mmm) REVERT: D 395 LYS cc_start: 0.8367 (mttt) cc_final: 0.7970 (mtmm) REVERT: D 485 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8549 (pp) REVERT: D 531 MET cc_start: 0.9085 (pmm) cc_final: 0.8853 (pmm) REVERT: D 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9503 (mmm) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 0.2990 time to fit residues: 50.2722 Evaluate side-chains 116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 C residue 145 PHE Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 62 optimal weight: 0.0970 chunk 150 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.064737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047298 restraints weight = 64911.766| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.90 r_work: 0.2758 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3281 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 : 0.535 8.555 20613 Z= 0.269 Chirality : 0.038 0.139 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.525 169.131 2100 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.61 % Allowed : 7.25 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.20), residues: 1863 helix: 2.81 (0.14), residues: 1296 sheet: 2.71 (0.72), residues: 48 loop : -0.42 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 264 HIS 0.004 0.001 HIS A 521 PHE 0.009 0.001 PHE D 270 TYR 0.009 0.001 TYR C 364 ARG 0.003 0.000 ARG B 420 Details of bonding type rmsd link_TRANS : bond 0.00073 ( 3) link_TRANS : angle 0.12093 ( 9) hydrogen bonds : bond 0.03093 ( 970) hydrogen bonds : angle 3.20545 ( 2853) covalent geometry : bond 0.00240 (15121) covalent geometry : angle 0.53464 (20604) *********************** 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 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.780 Fit side-chains REVERT: A 100 MET cc_start: 0.9162 (mmm) cc_final: 0.8819 (mmm) REVERT: A 240 MET cc_start: 0.8869 (mmm) cc_final: 0.8444 (tpp) REVERT: A 365 LYS cc_start: 0.9431 (tttt) cc_final: 0.9222 (tttt) REVERT: A 395 LYS cc_start: 0.8346 (mttt) cc_final: 0.7945 (mtmm) REVERT: A 485 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8141 (pp) REVERT: A 494 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8697 (pt) REVERT: A 541 MET cc_start: 0.9784 (mmm) cc_final: 0.9506 (mmm) REVERT: B 100 MET cc_start: 0.9168 (mmm) cc_final: 0.8824 (mmm) REVERT: B 240 MET cc_start: 0.8914 (mmm) cc_final: 0.8494 (tpp) REVERT: B 365 LYS cc_start: 0.9430 (tttt) cc_final: 0.9220 (tttt) REVERT: B 395 LYS cc_start: 0.8344 (mttt) cc_final: 0.7948 (mtmm) REVERT: B 485 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8531 (pp) REVERT: B 541 MET cc_start: 0.9779 (mmm) cc_final: 0.9494 (mmm) REVERT: C 100 MET cc_start: 0.9159 (mmm) cc_final: 0.8808 (mmm) REVERT: C 240 MET cc_start: 0.8894 (mmm) cc_final: 0.8475 (tpp) REVERT: C 365 LYS cc_start: 0.9431 (tttt) cc_final: 0.9220 (tttt) REVERT: C 395 LYS cc_start: 0.8352 (mttt) cc_final: 0.7951 (mtmm) REVERT: C 485 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8534 (pp) REVERT: C 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9484 (mmm) REVERT: D 100 MET cc_start: 0.9167 (mmm) cc_final: 0.8818 (mmm) REVERT: D 240 MET cc_start: 0.8892 (mmm) cc_final: 0.8476 (tpp) REVERT: D 365 LYS cc_start: 0.9430 (tttt) cc_final: 0.9220 (tttt) REVERT: D 395 LYS cc_start: 0.8339 (mttt) cc_final: 0.7947 (mtmm) REVERT: D 485 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8530 (pp) REVERT: D 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9497 (mmm) outliers start: 9 outliers final: 4 residues processed: 120 average time/residue: 0.3074 time to fit residues: 53.7415 Evaluate side-chains 117 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 2.319 ------------------------------------------------------------------------------- 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 C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.064944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047583 restraints weight = 64798.555| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.90 r_work: 0.2763 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3365 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 : 0.549 9.174 20613 Z= 0.272 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.508 168.992 2100 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.81 % Allowed : 6.71 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.20), residues: 1863 helix: 2.86 (0.14), residues: 1296 sheet: 2.66 (0.71), residues: 48 loop : -0.38 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 264 HIS 0.002 0.001 HIS B 308 PHE 0.009 0.001 PHE D 270 TYR 0.008 0.001 TYR A 364 ARG 0.002 0.000 ARG B 420 Details of bonding type rmsd link_TRANS : bond 0.00055 ( 3) link_TRANS : angle 0.12815 ( 9) hydrogen bonds : bond 0.03027 ( 970) hydrogen bonds : angle 3.16398 ( 2853) covalent geometry : bond 0.00243 (15121) covalent geometry : angle 0.54920 (20604) *********************** 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: 12 poor density : 113 time to evaluate : 1.709 Fit side-chains REVERT: A 100 MET cc_start: 0.9158 (mmm) cc_final: 0.8813 (mmm) REVERT: A 240 MET cc_start: 0.8913 (mmm) cc_final: 0.8506 (tpp) REVERT: A 395 LYS cc_start: 0.8339 (mttt) cc_final: 0.7942 (mtmm) REVERT: A 485 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8138 (pp) REVERT: A 494 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8684 (pt) REVERT: A 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9499 (mmm) REVERT: B 100 MET cc_start: 0.9168 (mmm) cc_final: 0.8822 (mmm) REVERT: B 240 MET cc_start: 0.8916 (mmm) cc_final: 0.8509 (tpp) REVERT: B 395 LYS cc_start: 0.8342 (mttt) cc_final: 0.7949 (mtmm) REVERT: B 485 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8555 (pp) REVERT: B 494 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8678 (pt) REVERT: B 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9498 (mmm) REVERT: C 100 MET cc_start: 0.9165 (mmm) cc_final: 0.8814 (mmm) REVERT: C 240 MET cc_start: 0.8900 (mmm) cc_final: 0.8492 (tpp) REVERT: C 395 LYS cc_start: 0.8344 (mttt) cc_final: 0.7947 (mtmm) REVERT: C 485 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8558 (pp) REVERT: C 494 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8679 (pt) REVERT: C 541 MET cc_start: 0.9775 (mmm) cc_final: 0.9490 (mmm) REVERT: D 100 MET cc_start: 0.9169 (mmm) cc_final: 0.8822 (mmm) REVERT: D 240 MET cc_start: 0.8898 (mmm) cc_final: 0.8492 (tpp) REVERT: D 395 LYS cc_start: 0.8339 (mttt) cc_final: 0.7952 (mtmm) REVERT: D 485 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8557 (pp) REVERT: D 494 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8682 (pt) REVERT: D 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9499 (mmm) outliers start: 12 outliers final: 4 residues processed: 125 average time/residue: 0.3019 time to fit residues: 54.7061 Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 177 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.062674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.045230 restraints weight = 65700.201| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.90 r_work: 0.2692 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3355 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= 0.210 Angle : 0.633 10.168 20613 Z= 0.318 Chirality : 0.040 0.138 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.490 168.137 2100 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.08 % Allowed : 6.51 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.20), residues: 1863 helix: 2.84 (0.14), residues: 1296 sheet: 2.44 (0.70), residues: 48 loop : -0.34 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.004 0.001 HIS A 345 PHE 0.010 0.001 PHE C 270 TYR 0.013 0.001 TYR A 511 ARG 0.016 0.000 ARG A 534 Details of bonding type rmsd link_TRANS : bond 0.00014 ( 3) link_TRANS : angle 0.11237 ( 9) hydrogen bonds : bond 0.03939 ( 970) hydrogen bonds : angle 3.45038 ( 2853) covalent geometry : bond 0.00467 (15121) covalent geometry : angle 0.63359 (20604) ********************** 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 128 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.548 Fit side-chains REVERT: A 100 MET cc_start: 0.9254 (mmm) cc_final: 0.8900 (mmm) REVERT: A 240 MET cc_start: 0.8927 (mmm) cc_final: 0.8361 (mmm) REVERT: A 395 LYS cc_start: 0.8532 (mttt) cc_final: 0.8091 (mtmm) REVERT: A 485 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8366 (pp) REVERT: A 494 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8926 (pt) REVERT: A 541 MET cc_start: 0.9787 (mmm) cc_final: 0.9502 (mmm) REVERT: B 100 MET cc_start: 0.9263 (mmm) cc_final: 0.8908 (mmm) REVERT: B 240 MET cc_start: 0.8928 (mmm) cc_final: 0.8363 (mmm) REVERT: B 395 LYS cc_start: 0.8517 (mttt) cc_final: 0.8080 (mtmm) REVERT: B 485 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8534 (pp) REVERT: B 494 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8931 (pt) REVERT: B 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9498 (mmm) REVERT: C 100 MET cc_start: 0.9257 (mmm) cc_final: 0.8896 (mmm) REVERT: C 240 MET cc_start: 0.8911 (mmm) cc_final: 0.8339 (mmm) REVERT: C 395 LYS cc_start: 0.8529 (mttt) cc_final: 0.8089 (mtmm) REVERT: C 485 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8540 (pp) REVERT: C 494 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8930 (pt) REVERT: C 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9493 (mmm) REVERT: D 100 MET cc_start: 0.9260 (mmm) cc_final: 0.8904 (mmm) REVERT: D 240 MET cc_start: 0.8910 (mmm) cc_final: 0.8341 (mmm) REVERT: D 395 LYS cc_start: 0.8518 (mttt) cc_final: 0.8084 (mtmm) REVERT: D 485 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8537 (pp) REVERT: D 494 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8931 (pt) REVERT: D 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9495 (mmm) outliers start: 16 outliers final: 8 residues processed: 124 average time/residue: 0.3191 time to fit residues: 58.0252 Evaluate side-chains 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 31 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 164 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 131 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.064325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047062 restraints weight = 65571.729| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.92 r_work: 0.2741 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3478 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 : 0.580 9.904 20613 Z= 0.286 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.550 169.781 2100 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.75 % Allowed : 6.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.20), residues: 1863 helix: 2.87 (0.14), residues: 1296 sheet: 2.47 (0.67), residues: 48 loop : -0.27 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 264 HIS 0.002 0.000 HIS A 390 PHE 0.009 0.001 PHE D 270 TYR 0.010 0.001 TYR A 364 ARG 0.012 0.000 ARG A 534 Details of bonding type rmsd link_TRANS : bond 0.00072 ( 3) link_TRANS : angle 0.13100 ( 9) hydrogen bonds : bond 0.03244 ( 970) hydrogen bonds : angle 3.25842 ( 2853) covalent geometry : bond 0.00261 (15121) covalent geometry : angle 0.58015 (20604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6020.78 seconds wall clock time: 105 minutes 20.41 seconds (6320.41 seconds total)