Starting phenix.real_space_refine on Fri Jun 13 07:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io0_35603/06_2025/8io0_35603_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io0_35603/06_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_35603/06_2025/8io0_35603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io0_35603/06_2025/8io0_35603.map" model { file = "/net/cci-nas-00/data/ceres_data/8io0_35603/06_2025/8io0_35603_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io0_35603/06_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-5710/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: 7.83, per 1000 atoms: 0.53 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: 3.29 Conformation dependent library (CDL) restraints added in 1.8 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: 1.48 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: 4.44 Time building geometry restraints manager: 3.95 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.290 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- 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 : 1.568 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: 0.3614 time to fit residues: 91.1908 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 : 1.825 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048058 restraints weight = 63473.633| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.89 r_work: 0.2787 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 1.674 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: 0.9075 (mmm) cc_final: 0.8578 (tpp) REVERT: A 257 MET cc_start: 0.9416 (tpp) cc_final: 0.9210 (tpp) REVERT: A 395 LYS cc_start: 0.7970 (mttt) cc_final: 0.7290 (mtpt) REVERT: A 465 MET cc_start: 0.9422 (ttm) cc_final: 0.9120 (ttt) REVERT: A 485 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8111 (pt) REVERT: A 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9504 (mmm) REVERT: B 100 MET cc_start: 0.9080 (mmm) cc_final: 0.8588 (tpp) REVERT: B 257 MET cc_start: 0.9408 (tpp) cc_final: 0.9198 (tpp) REVERT: B 395 LYS cc_start: 0.7960 (mttt) cc_final: 0.7284 (mtpt) REVERT: B 465 MET cc_start: 0.9411 (ttm) cc_final: 0.9101 (ttt) REVERT: B 485 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8231 (pt) REVERT: B 541 MET cc_start: 0.9772 (mmm) cc_final: 0.9487 (mmm) REVERT: C 100 MET cc_start: 0.9064 (mmm) cc_final: 0.8570 (tpp) REVERT: C 257 MET cc_start: 0.9418 (tpp) cc_final: 0.9209 (tpp) REVERT: C 395 LYS cc_start: 0.7979 (mttt) cc_final: 0.7304 (mtpt) REVERT: C 465 MET cc_start: 0.9414 (ttm) cc_final: 0.9110 (ttt) REVERT: C 485 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8235 (pt) REVERT: C 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9485 (mmm) REVERT: D 100 MET cc_start: 0.9067 (mmm) cc_final: 0.8577 (tpp) REVERT: D 257 MET cc_start: 0.9413 (tpp) cc_final: 0.9203 (tpp) REVERT: D 395 LYS cc_start: 0.7971 (mttt) cc_final: 0.7294 (mtpt) REVERT: D 465 MET cc_start: 0.9419 (ttm) cc_final: 0.9114 (ttt) REVERT: D 485 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8235 (pt) REVERT: D 541 MET cc_start: 0.9767 (mmm) cc_final: 0.9479 (mmm) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.3206 time to fit residues: 60.8778 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 : 1.756 ------------------------------------------------------------------------------- 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: 8.9990 chunk 169 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 7 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 overall best weight: 2.3884 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.064465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046956 restraints weight = 64953.721| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.95 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: 0.8513 moved from start: 0.2368 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= 0.140 Angle : 0.547 7.477 20613 Z= 0.285 Chirality : 0.038 0.114 2378 Planarity : 0.004 0.044 2540 Dihedral : 12.831 170.633 2100 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: 1.80 (0.19), residues: 1863 helix: 2.05 (0.14), residues: 1296 sheet: 1.88 (0.60), residues: 48 loop : -1.14 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 264 HIS 0.004 0.001 HIS B 239 PHE 0.011 0.001 PHE A 270 TYR 0.009 0.001 TYR C 511 ARG 0.006 0.000 ARG B 63 Details of bonding type rmsd link_TRANS : bond 0.00059 ( 3) link_TRANS : angle 0.05254 ( 9) hydrogen bonds : bond 0.03643 ( 970) hydrogen bonds : angle 3.42671 ( 2853) covalent geometry : bond 0.00304 (15121) covalent geometry : angle 0.54700 (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 : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9145 (mmm) cc_final: 0.8583 (tpp) REVERT: A 257 MET cc_start: 0.9442 (tpp) cc_final: 0.9238 (tpp) REVERT: A 365 LYS cc_start: 0.9385 (tttt) cc_final: 0.9181 (tttt) REVERT: A 395 LYS cc_start: 0.8226 (mttt) cc_final: 0.7527 (mtpt) REVERT: A 426 MET cc_start: 0.8435 (mmm) cc_final: 0.8116 (tpp) REVERT: A 485 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8279 (pp) REVERT: A 531 MET cc_start: 0.9057 (pmm) cc_final: 0.8584 (pmm) REVERT: A 541 MET cc_start: 0.9792 (mmm) cc_final: 0.9527 (mmm) REVERT: B 100 MET cc_start: 0.9152 (mmm) cc_final: 0.8595 (tpp) REVERT: B 257 MET cc_start: 0.9437 (tpp) cc_final: 0.9231 (tpp) REVERT: B 365 LYS cc_start: 0.9387 (tttt) cc_final: 0.9181 (tttt) REVERT: B 395 LYS cc_start: 0.8220 (mttt) cc_final: 0.7527 (mtpt) REVERT: B 426 MET cc_start: 0.8434 (mmm) cc_final: 0.8114 (tpp) REVERT: B 485 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8357 (pp) REVERT: B 531 MET cc_start: 0.9058 (pmm) cc_final: 0.8584 (pmm) REVERT: B 541 MET cc_start: 0.9783 (mmm) cc_final: 0.9511 (mmm) REVERT: C 100 MET cc_start: 0.9141 (mmm) cc_final: 0.8577 (tpp) REVERT: C 257 MET cc_start: 0.9437 (tpp) cc_final: 0.9230 (tpp) REVERT: C 365 LYS cc_start: 0.9392 (tttt) cc_final: 0.9188 (tttt) REVERT: C 395 LYS cc_start: 0.8221 (mttt) cc_final: 0.7525 (mtpt) REVERT: C 426 MET cc_start: 0.8438 (mmm) cc_final: 0.8119 (tpp) REVERT: C 485 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8354 (pp) REVERT: C 531 MET cc_start: 0.9072 (pmm) cc_final: 0.8602 (pmm) REVERT: C 541 MET cc_start: 0.9787 (mmm) cc_final: 0.9518 (mmm) REVERT: D 100 MET cc_start: 0.9145 (mmm) cc_final: 0.8586 (tpp) REVERT: D 257 MET cc_start: 0.9445 (tpp) cc_final: 0.9239 (tpp) REVERT: D 365 LYS cc_start: 0.9388 (tttt) cc_final: 0.9183 (tttt) REVERT: D 395 LYS cc_start: 0.8218 (mttt) cc_final: 0.7523 (mtpt) REVERT: D 426 MET cc_start: 0.8431 (mmm) cc_final: 0.8113 (tpp) REVERT: D 485 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8353 (pp) REVERT: D 531 MET cc_start: 0.9067 (pmm) cc_final: 0.8597 (pmm) REVERT: D 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9509 (mmm) outliers start: 8 outliers final: 4 residues processed: 116 average time/residue: 0.3181 time to fit residues: 55.1588 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 : 1.696 ------------------------------------------------------------------------------- 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: 9.9990 chunk 162 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.063703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.046234 restraints weight = 64659.538| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.93 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: 0.8525 moved from start: 0.2656 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 : 0.534 7.557 20613 Z= 0.279 Chirality : 0.038 0.118 2378 Planarity : 0.003 0.041 2540 Dihedral : 12.632 168.589 2100 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.36 % Allowed : 5.97 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.20), residues: 1863 helix: 2.49 (0.14), residues: 1296 sheet: 2.03 (0.62), residues: 48 loop : -0.88 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.004 0.001 HIS C 390 PHE 0.011 0.001 PHE D 270 TYR 0.010 0.001 TYR B 511 ARG 0.002 0.000 ARG D 507 Details of bonding type rmsd link_TRANS : bond 0.00063 ( 3) link_TRANS : angle 0.21575 ( 9) hydrogen bonds : bond 0.03541 ( 970) hydrogen bonds : angle 3.35005 ( 2853) covalent geometry : bond 0.00321 (15121) covalent geometry : angle 0.53424 (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 134 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9179 (mmm) cc_final: 0.8924 (mmm) REVERT: A 395 LYS cc_start: 0.8322 (mttt) cc_final: 0.7895 (mtmm) REVERT: A 426 MET cc_start: 0.8428 (mmm) cc_final: 0.8111 (tpp) REVERT: A 485 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8155 (pp) REVERT: A 531 MET cc_start: 0.9058 (pmm) cc_final: 0.8651 (pmm) REVERT: A 541 MET cc_start: 0.9786 (mmm) cc_final: 0.9521 (mmm) REVERT: B 100 MET cc_start: 0.9187 (mmm) cc_final: 0.8932 (mmm) REVERT: B 395 LYS cc_start: 0.8324 (mttt) cc_final: 0.7898 (mtmm) REVERT: B 426 MET cc_start: 0.8432 (mmm) cc_final: 0.8119 (tpp) REVERT: B 485 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8555 (pp) REVERT: B 531 MET cc_start: 0.9069 (pmm) cc_final: 0.8662 (pmm) REVERT: B 541 MET cc_start: 0.9784 (mmm) cc_final: 0.9517 (mmm) REVERT: C 100 MET cc_start: 0.9181 (mmm) cc_final: 0.8923 (mmm) REVERT: C 395 LYS cc_start: 0.8318 (mttt) cc_final: 0.7895 (mtmm) REVERT: C 426 MET cc_start: 0.8427 (mmm) cc_final: 0.8113 (tpp) REVERT: C 485 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8556 (pp) REVERT: C 531 MET cc_start: 0.9077 (pmm) cc_final: 0.8673 (pmm) REVERT: C 541 MET cc_start: 0.9784 (mmm) cc_final: 0.9517 (mmm) REVERT: D 100 MET cc_start: 0.9180 (mmm) cc_final: 0.8926 (mmm) REVERT: D 395 LYS cc_start: 0.8320 (mttt) cc_final: 0.7901 (mtmm) REVERT: D 426 MET cc_start: 0.8431 (mmm) cc_final: 0.8117 (tpp) REVERT: D 485 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8556 (pp) REVERT: D 531 MET cc_start: 0.9077 (pmm) cc_final: 0.8672 (pmm) REVERT: D 541 MET cc_start: 0.9785 (mmm) cc_final: 0.9518 (mmm) outliers start: 20 outliers final: 4 residues processed: 126 average time/residue: 0.4025 time to fit residues: 71.1842 Evaluate side-chains 112 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.063829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046417 restraints weight = 65472.783| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.93 r_work: 0.2730 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2884 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 : 0.536 7.539 20613 Z= 0.278 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.566 168.442 2100 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.54 % Allowed : 6.37 % 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: 2.65 (0.20), residues: 1863 helix: 2.66 (0.15), residues: 1296 sheet: 2.38 (0.67), residues: 48 loop : -0.74 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 264 HIS 0.005 0.001 HIS A 300 PHE 0.010 0.001 PHE B 270 TYR 0.010 0.001 TYR C 511 ARG 0.004 0.000 ARG C 420 Details of bonding type rmsd link_TRANS : bond 0.00069 ( 3) link_TRANS : angle 0.14125 ( 9) hydrogen bonds : bond 0.03481 ( 970) hydrogen bonds : angle 3.32431 ( 2853) covalent geometry : bond 0.00320 (15121) covalent geometry : angle 0.53587 (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 121 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9175 (mmm) cc_final: 0.8875 (mmm) REVERT: A 365 LYS cc_start: 0.9398 (tttt) cc_final: 0.9109 (tttt) REVERT: A 395 LYS cc_start: 0.8370 (mttt) cc_final: 0.7941 (mtmm) REVERT: A 443 LYS cc_start: 0.9603 (mttt) cc_final: 0.9339 (mtmm) REVERT: A 485 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8160 (pp) REVERT: A 531 MET cc_start: 0.9107 (pmm) cc_final: 0.8764 (pmm) REVERT: A 541 MET cc_start: 0.9786 (mmm) cc_final: 0.9516 (mmm) REVERT: B 100 MET cc_start: 0.9181 (mmm) cc_final: 0.8880 (mmm) REVERT: B 365 LYS cc_start: 0.9394 (tttt) cc_final: 0.9103 (tttt) REVERT: B 395 LYS cc_start: 0.8376 (mttt) cc_final: 0.7948 (mtmm) REVERT: B 443 LYS cc_start: 0.9599 (mttt) cc_final: 0.9338 (mtmm) REVERT: B 485 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8477 (pp) REVERT: B 531 MET cc_start: 0.9110 (pmm) cc_final: 0.8767 (pmm) REVERT: B 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9512 (mmm) REVERT: C 100 MET cc_start: 0.9169 (mmm) cc_final: 0.8865 (mmm) REVERT: C 365 LYS cc_start: 0.9401 (tttt) cc_final: 0.9112 (tttt) REVERT: C 395 LYS cc_start: 0.8371 (mttt) cc_final: 0.7941 (mtmm) REVERT: C 443 LYS cc_start: 0.9607 (mttt) cc_final: 0.9344 (mtmm) REVERT: C 485 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8471 (pp) REVERT: C 531 MET cc_start: 0.9118 (pmm) cc_final: 0.8775 (pmm) REVERT: C 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9512 (mmm) REVERT: D 100 MET cc_start: 0.9173 (mmm) cc_final: 0.8873 (mmm) REVERT: D 365 LYS cc_start: 0.9399 (tttt) cc_final: 0.9110 (tttt) REVERT: D 395 LYS cc_start: 0.8377 (mttt) cc_final: 0.7953 (mtmm) REVERT: D 443 LYS cc_start: 0.9601 (mttt) cc_final: 0.9335 (mtmm) REVERT: D 485 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8479 (pp) REVERT: D 531 MET cc_start: 0.9113 (pmm) cc_final: 0.8771 (pmm) REVERT: D 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9511 (mmm) outliers start: 8 outliers final: 4 residues processed: 121 average time/residue: 0.3946 time to fit residues: 69.7463 Evaluate side-chains 113 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 109 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.064661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047307 restraints weight = 64761.679| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.93 r_work: 0.2755 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15124 Z= 0.117 Angle : 0.522 7.425 20613 Z= 0.265 Chirality : 0.037 0.117 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.552 168.497 2100 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.08 % Allowed : 6.31 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.79 (0.20), residues: 1863 helix: 2.75 (0.14), residues: 1296 sheet: 2.76 (0.73), residues: 48 loop : -0.69 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 264 HIS 0.002 0.001 HIS C 308 PHE 0.009 0.001 PHE A 270 TYR 0.007 0.001 TYR B 511 ARG 0.003 0.000 ARG A 420 Details of bonding type rmsd link_TRANS : bond 0.00112 ( 3) link_TRANS : angle 0.27366 ( 9) hydrogen bonds : bond 0.03133 ( 970) hydrogen bonds : angle 3.21083 ( 2853) covalent geometry : bond 0.00247 (15121) covalent geometry : angle 0.52165 (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 126 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9157 (mmm) cc_final: 0.8833 (mmm) REVERT: A 365 LYS cc_start: 0.9371 (tttt) cc_final: 0.9118 (tttt) REVERT: A 395 LYS cc_start: 0.8341 (mttt) cc_final: 0.7928 (mtmm) REVERT: A 443 LYS cc_start: 0.9599 (mttt) cc_final: 0.9335 (mtmm) REVERT: A 485 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8137 (pp) REVERT: A 494 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8706 (pt) REVERT: A 531 MET cc_start: 0.9032 (pmm) cc_final: 0.8781 (pmm) REVERT: A 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9502 (mmm) REVERT: B 100 MET cc_start: 0.9166 (mmm) cc_final: 0.8839 (mmm) REVERT: B 365 LYS cc_start: 0.9370 (tttt) cc_final: 0.9117 (tttt) REVERT: B 395 LYS cc_start: 0.8346 (mttt) cc_final: 0.7937 (mtmm) REVERT: B 443 LYS cc_start: 0.9590 (mttt) cc_final: 0.9330 (mtmm) REVERT: B 485 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8533 (pp) REVERT: B 494 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8694 (pt) REVERT: B 531 MET cc_start: 0.9038 (pmm) cc_final: 0.8787 (pmm) REVERT: B 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9496 (mmm) REVERT: C 100 MET cc_start: 0.9161 (mmm) cc_final: 0.8832 (mmm) REVERT: C 365 LYS cc_start: 0.9373 (tttt) cc_final: 0.9121 (tttt) REVERT: C 395 LYS cc_start: 0.8345 (mttt) cc_final: 0.7936 (mtmm) REVERT: C 443 LYS cc_start: 0.9600 (mttt) cc_final: 0.9332 (mtmm) REVERT: C 485 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8528 (pp) REVERT: C 494 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8702 (pt) REVERT: C 531 MET cc_start: 0.9039 (pmm) cc_final: 0.8788 (pmm) REVERT: C 541 MET cc_start: 0.9778 (mmm) cc_final: 0.9498 (mmm) REVERT: D 100 MET cc_start: 0.9164 (mmm) cc_final: 0.8834 (mmm) REVERT: D 365 LYS cc_start: 0.9374 (tttt) cc_final: 0.9122 (tttt) REVERT: D 395 LYS cc_start: 0.8342 (mttt) cc_final: 0.7944 (mtmm) REVERT: D 443 LYS cc_start: 0.9592 (mttt) cc_final: 0.9327 (mtmm) REVERT: D 485 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8532 (pp) REVERT: D 494 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8703 (pt) REVERT: D 531 MET cc_start: 0.9038 (pmm) cc_final: 0.8788 (pmm) REVERT: D 541 MET cc_start: 0.9780 (mmm) cc_final: 0.9501 (mmm) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.3431 time to fit residues: 61.0286 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 : 1.538 ------------------------------------------------------------------------------- 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=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: 5.9990 chunk 52 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.062752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045227 restraints weight = 66146.326| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.94 r_work: 0.2699 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15124 Z= 0.176 Angle : 0.563 8.048 20613 Z= 0.291 Chirality : 0.039 0.118 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.493 168.792 2100 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.08 % Allowed : 6.71 % Favored : 92.20 % 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: 2.86 (0.20), residues: 1863 helix: 2.77 (0.14), residues: 1296 sheet: 2.84 (0.76), residues: 48 loop : -0.60 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 264 HIS 0.003 0.001 HIS A 390 PHE 0.010 0.001 PHE D 270 TYR 0.012 0.001 TYR A 511 ARG 0.003 0.000 ARG B 420 Details of bonding type rmsd link_TRANS : bond 0.00017 ( 3) link_TRANS : angle 0.17225 ( 9) hydrogen bonds : bond 0.03740 ( 970) hydrogen bonds : angle 3.39396 ( 2853) covalent geometry : bond 0.00389 (15121) covalent geometry : angle 0.56322 (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 126 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 2.188 Fit side-chains REVERT: A 100 MET cc_start: 0.9238 (mmm) cc_final: 0.8890 (mmm) REVERT: A 395 LYS cc_start: 0.8494 (mttt) cc_final: 0.8059 (mtmm) REVERT: A 443 LYS cc_start: 0.9617 (mttt) cc_final: 0.9334 (mtmm) REVERT: A 485 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8163 (pp) REVERT: A 494 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8887 (pt) REVERT: A 531 MET cc_start: 0.9082 (pmm) cc_final: 0.8854 (pmm) REVERT: A 541 MET cc_start: 0.9774 (mmm) cc_final: 0.9488 (mmm) REVERT: B 100 MET cc_start: 0.9241 (mmm) cc_final: 0.8894 (mmm) REVERT: B 395 LYS cc_start: 0.8486 (mttt) cc_final: 0.8054 (mtmm) REVERT: B 443 LYS cc_start: 0.9616 (mttt) cc_final: 0.9336 (mtmm) REVERT: B 485 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8512 (pp) REVERT: B 494 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8877 (pt) REVERT: B 531 MET cc_start: 0.9087 (pmm) cc_final: 0.8860 (pmm) REVERT: B 541 MET cc_start: 0.9775 (mmm) cc_final: 0.9494 (mmm) REVERT: C 100 MET cc_start: 0.9233 (mmm) cc_final: 0.8881 (mmm) REVERT: C 395 LYS cc_start: 0.8491 (mttt) cc_final: 0.8056 (mtmm) REVERT: C 443 LYS cc_start: 0.9615 (mttt) cc_final: 0.9329 (mtmm) REVERT: C 485 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8511 (pp) REVERT: C 494 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8881 (pt) REVERT: C 531 MET cc_start: 0.9090 (pmm) cc_final: 0.8863 (pmm) REVERT: C 541 MET cc_start: 0.9769 (mmm) cc_final: 0.9482 (mmm) REVERT: D 100 MET cc_start: 0.9232 (mmm) cc_final: 0.8882 (mmm) REVERT: D 395 LYS cc_start: 0.8484 (mttt) cc_final: 0.8054 (mtmm) REVERT: D 443 LYS cc_start: 0.9617 (mttt) cc_final: 0.9335 (mtmm) REVERT: D 485 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (pp) REVERT: D 494 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8880 (pt) REVERT: D 531 MET cc_start: 0.9093 (pmm) cc_final: 0.8864 (pmm) REVERT: D 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9497 (mmm) outliers start: 16 outliers final: 8 residues processed: 122 average time/residue: 0.3996 time to fit residues: 72.3922 Evaluate side-chains 123 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 62 optimal weight: 0.2980 chunk 150 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.063944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046468 restraints weight = 65472.283| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.94 r_work: 0.2729 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15124 Z= 0.130 Angle : 0.543 8.484 20613 Z= 0.276 Chirality : 0.038 0.126 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.517 169.178 2100 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.08 % Allowed : 6.98 % Favored : 91.93 % 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: 2.88 (0.76), residues: 48 loop : -0.41 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 264 HIS 0.003 0.001 HIS B 390 PHE 0.009 0.001 PHE B 270 TYR 0.009 0.001 TYR B 95 ARG 0.003 0.000 ARG A 420 Details of bonding type rmsd link_TRANS : bond 0.00052 ( 3) link_TRANS : angle 0.14599 ( 9) hydrogen bonds : bond 0.03345 ( 970) hydrogen bonds : angle 3.28653 ( 2853) covalent geometry : bond 0.00279 (15121) covalent geometry : angle 0.54311 (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 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.779 Fit side-chains REVERT: A 100 MET cc_start: 0.9205 (mmm) cc_final: 0.8846 (mmm) REVERT: A 395 LYS cc_start: 0.8410 (mttt) cc_final: 0.8002 (mtmm) REVERT: A 443 LYS cc_start: 0.9594 (mttt) cc_final: 0.9305 (mtmm) REVERT: A 485 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 494 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8796 (pt) REVERT: A 541 MET cc_start: 0.9778 (mmm) cc_final: 0.9494 (mmm) REVERT: B 100 MET cc_start: 0.9212 (mmm) cc_final: 0.8855 (mmm) REVERT: B 395 LYS cc_start: 0.8401 (mttt) cc_final: 0.8000 (mtmm) REVERT: B 443 LYS cc_start: 0.9595 (mttt) cc_final: 0.9339 (mtmm) REVERT: B 485 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 494 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8790 (pt) REVERT: B 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9489 (mmm) REVERT: C 100 MET cc_start: 0.9201 (mmm) cc_final: 0.8837 (mmm) REVERT: C 395 LYS cc_start: 0.8403 (mttt) cc_final: 0.7998 (mtmm) REVERT: C 443 LYS cc_start: 0.9596 (mttt) cc_final: 0.9333 (mtmm) REVERT: C 485 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8503 (pp) REVERT: C 494 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8795 (pt) REVERT: C 541 MET cc_start: 0.9766 (mmm) cc_final: 0.9475 (mmm) REVERT: D 100 MET cc_start: 0.9202 (mmm) cc_final: 0.8840 (mmm) REVERT: D 395 LYS cc_start: 0.8402 (mttt) cc_final: 0.8006 (mtmm) REVERT: D 443 LYS cc_start: 0.9595 (mttt) cc_final: 0.9338 (mtmm) REVERT: D 485 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8506 (pp) REVERT: D 494 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8794 (pt) REVERT: D 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9488 (mmm) outliers start: 16 outliers final: 8 residues processed: 120 average time/residue: 0.3048 time to fit residues: 53.0348 Evaluate side-chains 123 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 234 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 116 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.063975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046533 restraints weight = 65375.530| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.95 r_work: 0.2733 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15124 Z= 0.131 Angle : 0.558 9.144 20613 Z= 0.278 Chirality : 0.038 0.116 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.481 169.160 2100 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.36 % Allowed : 6.98 % Favored : 91.66 % 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: 3.05 (0.20), residues: 1863 helix: 2.87 (0.14), residues: 1296 sheet: 2.81 (0.76), residues: 48 loop : -0.36 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.002 0.001 HIS A 390 PHE 0.009 0.001 PHE B 270 TYR 0.009 0.001 TYR C 95 ARG 0.002 0.000 ARG B 420 Details of bonding type rmsd link_TRANS : bond 0.00056 ( 3) link_TRANS : angle 0.11114 ( 9) hydrogen bonds : bond 0.03254 ( 970) hydrogen bonds : angle 3.25361 ( 2853) covalent geometry : bond 0.00284 (15121) covalent geometry : angle 0.55812 (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 128 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.633 Fit side-chains REVERT: A 100 MET cc_start: 0.9208 (mmm) cc_final: 0.8847 (mmm) REVERT: A 395 LYS cc_start: 0.8415 (mttt) cc_final: 0.8010 (mtmm) REVERT: A 426 MET cc_start: 0.8310 (tpp) cc_final: 0.7894 (tpp) REVERT: A 443 LYS cc_start: 0.9590 (mttt) cc_final: 0.9299 (mtmm) REVERT: A 485 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8161 (pp) REVERT: A 494 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8805 (pt) REVERT: A 541 MET cc_start: 0.9782 (mmm) cc_final: 0.9498 (mmm) REVERT: B 100 MET cc_start: 0.9213 (mmm) cc_final: 0.8855 (mmm) REVERT: B 395 LYS cc_start: 0.8403 (mttt) cc_final: 0.8006 (mtmm) REVERT: B 426 MET cc_start: 0.8316 (tpp) cc_final: 0.7900 (tpp) REVERT: B 443 LYS cc_start: 0.9590 (mttt) cc_final: 0.9303 (mtmm) REVERT: B 485 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 494 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8876 (pt) REVERT: B 541 MET cc_start: 0.9781 (mmm) cc_final: 0.9496 (mmm) REVERT: C 100 MET cc_start: 0.9201 (mmm) cc_final: 0.8837 (mmm) REVERT: C 240 MET cc_start: 0.8896 (mmm) cc_final: 0.8425 (mmm) REVERT: C 395 LYS cc_start: 0.8408 (mttt) cc_final: 0.8004 (mtmm) REVERT: C 426 MET cc_start: 0.8312 (tpp) cc_final: 0.7896 (tpp) REVERT: C 443 LYS cc_start: 0.9592 (mttt) cc_final: 0.9300 (mtmm) REVERT: C 485 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 494 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8881 (pt) REVERT: C 541 MET cc_start: 0.9767 (mmm) cc_final: 0.9473 (mmm) REVERT: D 100 MET cc_start: 0.9203 (mmm) cc_final: 0.8842 (mmm) REVERT: D 240 MET cc_start: 0.8904 (mmm) cc_final: 0.8436 (mmm) REVERT: D 395 LYS cc_start: 0.8400 (mttt) cc_final: 0.8009 (mtmm) REVERT: D 426 MET cc_start: 0.8315 (tpp) cc_final: 0.7902 (tpp) REVERT: D 443 LYS cc_start: 0.9593 (mttt) cc_final: 0.9303 (mtmm) REVERT: D 485 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8505 (pp) REVERT: D 494 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8880 (pt) REVERT: D 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9487 (mmm) outliers start: 20 outliers final: 8 residues processed: 124 average time/residue: 0.2940 time to fit residues: 52.9931 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 : 1.759 ------------------------------------------------------------------------------- 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 177 optimal weight: 0.0020 chunk 13 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 overall best weight: 2.9594 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.063106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.045722 restraints weight = 65273.143| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.90 r_work: 0.2707 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15124 Z= 0.154 Angle : 0.587 9.182 20613 Z= 0.292 Chirality : 0.039 0.131 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.476 169.180 2100 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.36 % Allowed : 6.98 % Favored : 91.66 % 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: 2.88 (0.14), residues: 1296 sheet: 2.74 (0.75), residues: 48 loop : -0.33 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.003 0.001 HIS D 345 PHE 0.009 0.001 PHE C 270 TYR 0.010 0.001 TYR D 364 ARG 0.002 0.000 ARG B 420 Details of bonding type rmsd link_TRANS : bond 0.00028 ( 3) link_TRANS : angle 0.14379 ( 9) hydrogen bonds : bond 0.03548 ( 970) hydrogen bonds : angle 3.32457 ( 2853) covalent geometry : bond 0.00341 (15121) covalent geometry : angle 0.58677 (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 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 2.175 Fit side-chains REVERT: A 100 MET cc_start: 0.9238 (mmm) cc_final: 0.8865 (mmm) REVERT: A 168 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8666 (t80) REVERT: A 395 LYS cc_start: 0.8509 (mttt) cc_final: 0.8089 (mtmm) REVERT: A 485 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8265 (pp) REVERT: A 494 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8895 (pt) REVERT: A 541 MET cc_start: 0.9776 (mmm) cc_final: 0.9488 (mmm) REVERT: B 100 MET cc_start: 0.9242 (mmm) cc_final: 0.8873 (mmm) REVERT: B 168 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8669 (t80) REVERT: B 395 LYS cc_start: 0.8494 (mttt) cc_final: 0.8081 (mtmm) REVERT: B 443 LYS cc_start: 0.9601 (mttt) cc_final: 0.9315 (mtmm) REVERT: B 485 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8526 (pp) REVERT: B 494 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8889 (pt) REVERT: B 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9489 (mmm) REVERT: C 100 MET cc_start: 0.9237 (mmm) cc_final: 0.8862 (mmm) REVERT: C 168 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.8671 (t80) REVERT: C 395 LYS cc_start: 0.8502 (mttt) cc_final: 0.8083 (mtmm) REVERT: C 443 LYS cc_start: 0.9567 (mttt) cc_final: 0.9273 (mtmm) REVERT: C 485 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8524 (pp) REVERT: C 494 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8890 (pt) REVERT: C 541 MET cc_start: 0.9771 (mmm) cc_final: 0.9480 (mmm) REVERT: D 100 MET cc_start: 0.9240 (mmm) cc_final: 0.8868 (mmm) REVERT: D 168 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8667 (t80) REVERT: D 395 LYS cc_start: 0.8491 (mttt) cc_final: 0.8083 (mtmm) REVERT: D 443 LYS cc_start: 0.9567 (mttt) cc_final: 0.9278 (mtmm) REVERT: D 485 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8525 (pp) REVERT: D 494 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8890 (pt) REVERT: D 541 MET cc_start: 0.9777 (mmm) cc_final: 0.9488 (mmm) outliers start: 20 outliers final: 8 residues processed: 120 average time/residue: 0.3798 time to fit residues: 68.8025 Evaluate side-chains 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 168 TYR 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 168 TYR 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 168 TYR 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 168 TYR 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: 9.9990 chunk 137 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.063960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046515 restraints weight = 65320.811| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.92 r_work: 0.2729 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15124 Z= 0.129 Angle : 0.577 10.515 20613 Z= 0.282 Chirality : 0.038 0.122 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.493 169.765 2100 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.08 % Allowed : 7.32 % Favored : 91.59 % 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: 3.11 (0.20), residues: 1863 helix: 2.90 (0.14), residues: 1296 sheet: 2.67 (0.73), residues: 48 loop : -0.27 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 264 HIS 0.003 0.001 HIS A 521 PHE 0.010 0.001 PHE A 270 TYR 0.010 0.001 TYR A 364 ARG 0.002 0.000 ARG A 420 Details of bonding type rmsd link_TRANS : bond 0.00059 ( 3) link_TRANS : angle 0.13090 ( 9) hydrogen bonds : bond 0.03217 ( 970) hydrogen bonds : angle 3.23373 ( 2853) covalent geometry : bond 0.00280 (15121) covalent geometry : angle 0.57668 (20604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7722.46 seconds wall clock time: 140 minutes 12.48 seconds (8412.48 seconds total)