Starting phenix.real_space_refine on Tue Dec 31 04:44:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8io0_35603/12_2024/8io0_35603_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8io0_35603/12_2024/8io0_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_35603/12_2024/8io0_35603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8io0_35603/12_2024/8io0_35603.map" model { file = "/net/cci-nas-00/data/ceres_data/8io0_35603/12_2024/8io0_35603_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8io0_35603/12_2024/8io0_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.89, per 1000 atoms: 0.54 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: 3.59 Conformation dependent library (CDL) restraints added in 2.0 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: 1.72 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: 4.62 Time building geometry restraints manager: 4.15 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 33.400 Find NCS groups from input model: 0.830 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- 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 15121 Z= 0.546 Angle : 0.964 9.629 20604 Z= 0.546 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 *********************** 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 : 1.694 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: 0.3762 time to fit residues: 95.2947 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 : 1.926 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 15121 Z= 0.152 Angle : 0.562 8.255 20604 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 *********************** 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 : 1.796 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: 0.8977 (mmm) cc_final: 0.8365 (tpp) REVERT: A 257 MET cc_start: 0.9110 (tpp) cc_final: 0.8835 (tpp) REVERT: A 395 LYS cc_start: 0.8139 (mttt) cc_final: 0.7480 (mtpt) REVERT: A 465 MET cc_start: 0.9238 (ttm) cc_final: 0.8903 (ttt) REVERT: A 485 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8070 (pt) REVERT: A 541 MET cc_start: 0.9729 (mmm) cc_final: 0.9447 (mmm) REVERT: B 100 MET cc_start: 0.8971 (mmm) cc_final: 0.8357 (tpp) REVERT: B 257 MET cc_start: 0.9109 (tpp) cc_final: 0.8835 (tpp) REVERT: B 395 LYS cc_start: 0.8129 (mttt) cc_final: 0.7471 (mtpt) REVERT: B 465 MET cc_start: 0.9239 (ttm) cc_final: 0.8903 (ttt) REVERT: B 485 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8212 (pt) REVERT: B 541 MET cc_start: 0.9729 (mmm) cc_final: 0.9446 (mmm) REVERT: C 100 MET cc_start: 0.8971 (mmm) cc_final: 0.8356 (tpp) REVERT: C 257 MET cc_start: 0.9110 (tpp) cc_final: 0.8836 (tpp) REVERT: C 395 LYS cc_start: 0.8137 (mttt) cc_final: 0.7477 (mtpt) REVERT: C 465 MET cc_start: 0.9237 (ttm) cc_final: 0.8902 (ttt) REVERT: C 485 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8210 (pt) REVERT: C 541 MET cc_start: 0.9731 (mmm) cc_final: 0.9449 (mmm) REVERT: D 100 MET cc_start: 0.8968 (mmm) cc_final: 0.8353 (tpp) REVERT: D 257 MET cc_start: 0.9109 (tpp) cc_final: 0.8835 (tpp) REVERT: D 395 LYS cc_start: 0.8129 (mttt) cc_final: 0.7468 (mtpt) REVERT: D 465 MET cc_start: 0.9242 (ttm) cc_final: 0.8904 (ttt) REVERT: D 485 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8210 (pt) REVERT: D 541 MET cc_start: 0.9730 (mmm) cc_final: 0.9447 (mmm) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.3402 time to fit residues: 64.9786 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 : 1.880 ------------------------------------------------------------------------------- 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 94 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15121 Z= 0.353 Angle : 0.646 7.850 20604 Z= 0.340 Chirality : 0.041 0.115 2378 Planarity : 0.004 0.051 2540 Dihedral : 12.846 171.323 2100 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.81 % Allowed : 6.24 % 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: 1.73 (0.19), residues: 1863 helix: 1.99 (0.14), residues: 1296 sheet: 1.76 (0.60), residues: 48 loop : -1.11 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 264 HIS 0.005 0.001 HIS C 390 PHE 0.013 0.002 PHE B 94 TYR 0.014 0.002 TYR C 511 ARG 0.002 0.000 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.623 Fit side-chains REVERT: A 257 MET cc_start: 0.9188 (tpp) cc_final: 0.8919 (tpp) REVERT: A 365 LYS cc_start: 0.9401 (tttt) cc_final: 0.9130 (tttt) REVERT: A 395 LYS cc_start: 0.8586 (mttt) cc_final: 0.8175 (mtmm) REVERT: A 443 LYS cc_start: 0.9563 (mttt) cc_final: 0.9307 (mtmm) REVERT: A 465 MET cc_start: 0.9248 (ttm) cc_final: 0.8998 (ttt) REVERT: A 485 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8183 (pp) REVERT: A 531 MET cc_start: 0.8894 (pmm) cc_final: 0.8330 (pmm) REVERT: A 541 MET cc_start: 0.9740 (mmm) cc_final: 0.9474 (mmm) REVERT: B 257 MET cc_start: 0.9186 (tpp) cc_final: 0.8919 (tpp) REVERT: B 365 LYS cc_start: 0.9402 (tttt) cc_final: 0.9130 (tttt) REVERT: B 395 LYS cc_start: 0.8584 (mttt) cc_final: 0.8171 (mtmm) REVERT: B 443 LYS cc_start: 0.9565 (mttt) cc_final: 0.9316 (mtmm) REVERT: B 465 MET cc_start: 0.9249 (ttm) cc_final: 0.8998 (ttt) REVERT: B 485 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8269 (pp) REVERT: B 531 MET cc_start: 0.8897 (pmm) cc_final: 0.8333 (pmm) REVERT: B 541 MET cc_start: 0.9744 (mmm) cc_final: 0.9484 (mmm) REVERT: C 257 MET cc_start: 0.9191 (tpp) cc_final: 0.8922 (tpp) REVERT: C 365 LYS cc_start: 0.9402 (tttt) cc_final: 0.9132 (tttt) REVERT: C 395 LYS cc_start: 0.8583 (mttt) cc_final: 0.8171 (mtmm) REVERT: C 443 LYS cc_start: 0.9562 (mttt) cc_final: 0.9313 (mtmm) REVERT: C 465 MET cc_start: 0.9247 (ttm) cc_final: 0.8998 (ttt) REVERT: C 485 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8267 (pp) REVERT: C 531 MET cc_start: 0.8892 (pmm) cc_final: 0.8327 (pmm) REVERT: C 541 MET cc_start: 0.9745 (mmm) cc_final: 0.9486 (mmm) REVERT: D 257 MET cc_start: 0.9189 (tpp) cc_final: 0.8920 (tpp) REVERT: D 365 LYS cc_start: 0.9401 (tttt) cc_final: 0.9130 (tttt) REVERT: D 395 LYS cc_start: 0.8576 (mttt) cc_final: 0.8167 (mtmm) REVERT: D 443 LYS cc_start: 0.9563 (mttt) cc_final: 0.9315 (mtmm) REVERT: D 465 MET cc_start: 0.9246 (ttm) cc_final: 0.8996 (ttt) REVERT: D 485 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8267 (pp) REVERT: D 531 MET cc_start: 0.8897 (pmm) cc_final: 0.8334 (pmm) REVERT: D 541 MET cc_start: 0.9744 (mmm) cc_final: 0.9484 (mmm) outliers start: 12 outliers final: 4 residues processed: 120 average time/residue: 0.3020 time to fit residues: 52.6819 Evaluate side-chains 116 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.853 ------------------------------------------------------------------------------- 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 168 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15121 Z= 0.161 Angle : 0.536 7.385 20604 Z= 0.274 Chirality : 0.037 0.115 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.753 170.206 2100 Min Nonbonded Distance : 2.657 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.81 % Allowed : 5.97 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.36 (0.20), residues: 1863 helix: 2.44 (0.15), residues: 1296 sheet: 2.08 (0.62), residues: 48 loop : -0.85 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 264 HIS 0.003 0.001 HIS C 308 PHE 0.010 0.001 PHE B 270 TYR 0.008 0.001 TYR C 364 ARG 0.001 0.000 ARG D 507 *********************** 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 127 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8915 (mmp) cc_final: 0.8501 (mmm) REVERT: A 257 MET cc_start: 0.9025 (tpp) cc_final: 0.8746 (tpp) REVERT: A 365 LYS cc_start: 0.9397 (tttt) cc_final: 0.9124 (tttt) REVERT: A 465 MET cc_start: 0.9199 (ttm) cc_final: 0.8987 (ttt) REVERT: A 485 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8151 (pp) REVERT: A 531 MET cc_start: 0.8826 (pmm) cc_final: 0.8477 (pmm) REVERT: A 541 MET cc_start: 0.9733 (mmm) cc_final: 0.9460 (mmm) REVERT: B 100 MET cc_start: 0.8910 (mmp) cc_final: 0.8495 (mmm) REVERT: B 257 MET cc_start: 0.9022 (tpp) cc_final: 0.8744 (tpp) REVERT: B 365 LYS cc_start: 0.9400 (tttt) cc_final: 0.9126 (tttt) REVERT: B 465 MET cc_start: 0.9199 (ttm) cc_final: 0.8986 (ttt) REVERT: B 485 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8411 (pp) REVERT: B 531 MET cc_start: 0.8830 (pmm) cc_final: 0.8458 (pmm) REVERT: B 541 MET cc_start: 0.9732 (mmm) cc_final: 0.9458 (mmm) REVERT: C 100 MET cc_start: 0.8910 (mmp) cc_final: 0.8496 (mmm) REVERT: C 257 MET cc_start: 0.9025 (tpp) cc_final: 0.8745 (tpp) REVERT: C 365 LYS cc_start: 0.9400 (tttt) cc_final: 0.9128 (tttt) REVERT: C 465 MET cc_start: 0.9197 (ttm) cc_final: 0.8986 (ttt) REVERT: C 485 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8410 (pp) REVERT: C 531 MET cc_start: 0.8823 (pmm) cc_final: 0.8452 (pmm) REVERT: C 541 MET cc_start: 0.9734 (mmm) cc_final: 0.9460 (mmm) REVERT: D 100 MET cc_start: 0.8905 (mmp) cc_final: 0.8491 (mmm) REVERT: D 257 MET cc_start: 0.9025 (tpp) cc_final: 0.8745 (tpp) REVERT: D 365 LYS cc_start: 0.9399 (tttt) cc_final: 0.9125 (tttt) REVERT: D 465 MET cc_start: 0.9199 (ttm) cc_final: 0.8984 (ttt) REVERT: D 485 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8410 (pp) REVERT: D 531 MET cc_start: 0.8832 (pmm) cc_final: 0.8483 (pmm) REVERT: D 541 MET cc_start: 0.9732 (mmm) cc_final: 0.9457 (mmm) outliers start: 12 outliers final: 0 residues processed: 123 average time/residue: 0.3434 time to fit residues: 59.6618 Evaluate side-chains 112 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.780 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.0980 chunk 103 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 0.0270 chunk 74 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.8244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15121 Z= 0.215 Angle : 0.558 7.600 20604 Z= 0.285 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.628 169.092 2100 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.36 % Allowed : 6.17 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.20), residues: 1863 helix: 2.63 (0.15), residues: 1296 sheet: 2.49 (0.67), residues: 48 loop : -0.71 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 264 HIS 0.003 0.001 HIS B 390 PHE 0.010 0.001 PHE B 270 TYR 0.010 0.001 TYR D 511 ARG 0.003 0.000 ARG D 420 *********************** 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 136 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.782 Fit side-chains REVERT: A 100 MET cc_start: 0.9042 (mmp) cc_final: 0.8652 (mmm) REVERT: A 257 MET cc_start: 0.9045 (tpp) cc_final: 0.8760 (tpp) REVERT: A 365 LYS cc_start: 0.9398 (tttt) cc_final: 0.9141 (tttt) REVERT: A 395 LYS cc_start: 0.8560 (mttt) cc_final: 0.8151 (mtmm) REVERT: A 426 MET cc_start: 0.8406 (tpp) cc_final: 0.8057 (tpp) REVERT: A 443 LYS cc_start: 0.9531 (mttt) cc_final: 0.9207 (mtmm) REVERT: A 485 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8102 (pp) REVERT: A 494 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8871 (pt) REVERT: A 531 MET cc_start: 0.8830 (pmm) cc_final: 0.8478 (pmm) REVERT: A 532 MET cc_start: 0.9505 (mmm) cc_final: 0.9281 (mmm) REVERT: A 541 MET cc_start: 0.9735 (mmm) cc_final: 0.9462 (mmm) REVERT: B 100 MET cc_start: 0.9037 (mmp) cc_final: 0.8646 (mmm) REVERT: B 257 MET cc_start: 0.9044 (tpp) cc_final: 0.8760 (tpp) REVERT: B 365 LYS cc_start: 0.9400 (tttt) cc_final: 0.9141 (tttt) REVERT: B 395 LYS cc_start: 0.8557 (mttt) cc_final: 0.8147 (mtmm) REVERT: B 426 MET cc_start: 0.8410 (tpp) cc_final: 0.8061 (tpp) REVERT: B 443 LYS cc_start: 0.9534 (mttt) cc_final: 0.9212 (mtmm) REVERT: B 485 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8424 (pp) REVERT: B 494 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8868 (pt) REVERT: B 531 MET cc_start: 0.8835 (pmm) cc_final: 0.8484 (pmm) REVERT: B 532 MET cc_start: 0.9504 (mmm) cc_final: 0.9279 (mmm) REVERT: B 541 MET cc_start: 0.9734 (mmm) cc_final: 0.9460 (mmm) REVERT: C 100 MET cc_start: 0.9036 (mmp) cc_final: 0.8645 (mmm) REVERT: C 257 MET cc_start: 0.9047 (tpp) cc_final: 0.8759 (tpp) REVERT: C 365 LYS cc_start: 0.9400 (tttt) cc_final: 0.9143 (tttt) REVERT: C 395 LYS cc_start: 0.8558 (mttt) cc_final: 0.8150 (mtmm) REVERT: C 426 MET cc_start: 0.8409 (tpp) cc_final: 0.8060 (tpp) REVERT: C 443 LYS cc_start: 0.9531 (mttt) cc_final: 0.9208 (mtmm) REVERT: C 485 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8422 (pp) REVERT: C 494 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8869 (pt) REVERT: C 531 MET cc_start: 0.8828 (pmm) cc_final: 0.8476 (pmm) REVERT: C 532 MET cc_start: 0.9508 (mmm) cc_final: 0.9280 (mmm) REVERT: C 541 MET cc_start: 0.9735 (mmm) cc_final: 0.9462 (mmm) REVERT: D 100 MET cc_start: 0.9034 (mmp) cc_final: 0.8643 (mmm) REVERT: D 257 MET cc_start: 0.9046 (tpp) cc_final: 0.8760 (tpp) REVERT: D 365 LYS cc_start: 0.9400 (tttt) cc_final: 0.9142 (tttt) REVERT: D 395 LYS cc_start: 0.8552 (mttt) cc_final: 0.8144 (mtmm) REVERT: D 426 MET cc_start: 0.8408 (tpp) cc_final: 0.8060 (tpp) REVERT: D 443 LYS cc_start: 0.9532 (mttt) cc_final: 0.9210 (mtmm) REVERT: D 485 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8420 (pp) REVERT: D 494 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8867 (pt) REVERT: D 531 MET cc_start: 0.8836 (pmm) cc_final: 0.8484 (pmm) REVERT: D 532 MET cc_start: 0.9504 (mmm) cc_final: 0.9277 (mmm) REVERT: D 541 MET cc_start: 0.9734 (mmm) cc_final: 0.9459 (mmm) outliers start: 20 outliers final: 8 residues processed: 128 average time/residue: 0.3142 time to fit residues: 58.9360 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 : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 234 TRP Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 234 TRP Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 234 TRP Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 234 TRP Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15121 Z= 0.281 Angle : 0.588 7.576 20604 Z= 0.303 Chirality : 0.039 0.117 2378 Planarity : 0.003 0.042 2540 Dihedral : 12.604 169.241 2100 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.08 % Allowed : 5.90 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.20), residues: 1863 helix: 2.67 (0.15), residues: 1296 sheet: 2.62 (0.71), residues: 48 loop : -0.60 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 264 HIS 0.007 0.001 HIS D 300 PHE 0.010 0.001 PHE D 270 TYR 0.013 0.001 TYR A 511 ARG 0.002 0.000 ARG A 420 *********************** 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 136 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.865 Fit side-chains REVERT: A 100 MET cc_start: 0.9094 (mmp) cc_final: 0.8493 (mmm) REVERT: A 257 MET cc_start: 0.9086 (tpp) cc_final: 0.8809 (tpp) REVERT: A 365 LYS cc_start: 0.9405 (tttt) cc_final: 0.9139 (tttt) REVERT: A 395 LYS cc_start: 0.8634 (mttt) cc_final: 0.8219 (mtmm) REVERT: A 426 MET cc_start: 0.8503 (tpp) cc_final: 0.8187 (tpp) REVERT: A 443 LYS cc_start: 0.9566 (mttt) cc_final: 0.9237 (mtmm) REVERT: A 485 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 494 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8996 (pt) REVERT: A 531 MET cc_start: 0.8845 (pmm) cc_final: 0.8572 (pmm) REVERT: A 532 MET cc_start: 0.9534 (mmm) cc_final: 0.9310 (mmm) REVERT: A 541 MET cc_start: 0.9734 (mmm) cc_final: 0.9462 (mmm) REVERT: B 100 MET cc_start: 0.9089 (mmp) cc_final: 0.8487 (mmm) REVERT: B 257 MET cc_start: 0.9086 (tpp) cc_final: 0.8806 (tpp) REVERT: B 365 LYS cc_start: 0.9405 (tttt) cc_final: 0.9137 (tttt) REVERT: B 395 LYS cc_start: 0.8631 (mttt) cc_final: 0.8215 (mtmm) REVERT: B 426 MET cc_start: 0.8506 (tpp) cc_final: 0.8189 (tpp) REVERT: B 443 LYS cc_start: 0.9568 (mttt) cc_final: 0.9239 (mtmm) REVERT: B 485 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 494 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8988 (pt) REVERT: B 531 MET cc_start: 0.8850 (pmm) cc_final: 0.8551 (pmm) REVERT: B 532 MET cc_start: 0.9533 (mmm) cc_final: 0.9295 (mmm) REVERT: B 541 MET cc_start: 0.9733 (mmm) cc_final: 0.9459 (mmm) REVERT: C 100 MET cc_start: 0.9091 (mmp) cc_final: 0.8487 (mmm) REVERT: C 257 MET cc_start: 0.9088 (tpp) cc_final: 0.8811 (tpp) REVERT: C 365 LYS cc_start: 0.9405 (tttt) cc_final: 0.9140 (tttt) REVERT: C 395 LYS cc_start: 0.8634 (mttt) cc_final: 0.8219 (mtmm) REVERT: C 426 MET cc_start: 0.8505 (tpp) cc_final: 0.8190 (tpp) REVERT: C 443 LYS cc_start: 0.9564 (mttt) cc_final: 0.9236 (mtmm) REVERT: C 485 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8367 (pp) REVERT: C 494 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8989 (pt) REVERT: C 531 MET cc_start: 0.8844 (pmm) cc_final: 0.8545 (pmm) REVERT: C 532 MET cc_start: 0.9537 (mmm) cc_final: 0.9296 (mmm) REVERT: C 541 MET cc_start: 0.9735 (mmm) cc_final: 0.9461 (mmm) REVERT: D 100 MET cc_start: 0.9086 (mmp) cc_final: 0.8484 (mmm) REVERT: D 257 MET cc_start: 0.9087 (tpp) cc_final: 0.8810 (tpp) REVERT: D 365 LYS cc_start: 0.9405 (tttt) cc_final: 0.9138 (tttt) REVERT: D 395 LYS cc_start: 0.8626 (mttt) cc_final: 0.8214 (mtmm) REVERT: D 426 MET cc_start: 0.8508 (tpp) cc_final: 0.8192 (tpp) REVERT: D 443 LYS cc_start: 0.9566 (mttt) cc_final: 0.9239 (mtmm) REVERT: D 485 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8363 (pp) REVERT: D 494 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8988 (pt) REVERT: D 531 MET cc_start: 0.8850 (pmm) cc_final: 0.8551 (pmm) REVERT: D 532 MET cc_start: 0.9533 (mmm) cc_final: 0.9293 (mmm) REVERT: D 541 MET cc_start: 0.9732 (mmm) cc_final: 0.9458 (mmm) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 0.3046 time to fit residues: 58.6355 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 : 1.850 ------------------------------------------------------------------------------- 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 175 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 0.1980 chunk 101 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15121 Z= 0.157 Angle : 0.525 7.994 20604 Z= 0.268 Chirality : 0.038 0.116 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.572 169.109 2100 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: 2.92 (0.20), residues: 1863 helix: 2.79 (0.14), residues: 1296 sheet: 2.87 (0.73), residues: 48 loop : -0.48 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 264 HIS 0.003 0.001 HIS C 308 PHE 0.009 0.001 PHE D 270 TYR 0.009 0.001 TYR D 95 ARG 0.003 0.000 ARG D 420 *********************** 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 124 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.949 Fit side-chains REVERT: A 100 MET cc_start: 0.9012 (mmp) cc_final: 0.8638 (mmm) REVERT: A 257 MET cc_start: 0.9035 (tpp) cc_final: 0.8759 (tpp) REVERT: A 365 LYS cc_start: 0.9416 (tttt) cc_final: 0.9073 (tttt) REVERT: A 395 LYS cc_start: 0.8530 (mttt) cc_final: 0.8139 (mtmm) REVERT: A 443 LYS cc_start: 0.9520 (mttt) cc_final: 0.9219 (mtmm) REVERT: A 485 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8179 (pp) REVERT: A 494 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8887 (pt) REVERT: A 531 MET cc_start: 0.8739 (pmm) cc_final: 0.8525 (pmm) REVERT: A 532 MET cc_start: 0.9494 (mmm) cc_final: 0.9293 (mmm) REVERT: A 541 MET cc_start: 0.9727 (mmm) cc_final: 0.9445 (mmm) REVERT: B 100 MET cc_start: 0.9007 (mmp) cc_final: 0.8630 (mmm) REVERT: B 257 MET cc_start: 0.9034 (tpp) cc_final: 0.8758 (tpp) REVERT: B 365 LYS cc_start: 0.9418 (tttt) cc_final: 0.9075 (tttt) REVERT: B 395 LYS cc_start: 0.8528 (mttt) cc_final: 0.8135 (mtmm) REVERT: B 443 LYS cc_start: 0.9524 (mttt) cc_final: 0.9224 (mtmm) REVERT: B 485 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8389 (pp) REVERT: B 494 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8887 (pt) REVERT: B 531 MET cc_start: 0.8743 (pmm) cc_final: 0.8528 (pmm) REVERT: B 532 MET cc_start: 0.9493 (mmm) cc_final: 0.9292 (mmm) REVERT: B 541 MET cc_start: 0.9727 (mmm) cc_final: 0.9444 (mmm) REVERT: C 100 MET cc_start: 0.9007 (mmp) cc_final: 0.8632 (mmm) REVERT: C 257 MET cc_start: 0.9036 (tpp) cc_final: 0.8760 (tpp) REVERT: C 365 LYS cc_start: 0.9417 (tttt) cc_final: 0.9076 (tttt) REVERT: C 395 LYS cc_start: 0.8529 (mttt) cc_final: 0.8137 (mtmm) REVERT: C 443 LYS cc_start: 0.9520 (mttt) cc_final: 0.9218 (mtmm) REVERT: C 485 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8387 (pp) REVERT: C 494 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8887 (pt) REVERT: C 531 MET cc_start: 0.8736 (pmm) cc_final: 0.8523 (pmm) REVERT: C 532 MET cc_start: 0.9496 (mmm) cc_final: 0.9292 (mmm) REVERT: C 541 MET cc_start: 0.9728 (mmm) cc_final: 0.9445 (mmm) REVERT: D 100 MET cc_start: 0.9004 (mmp) cc_final: 0.8630 (mmm) REVERT: D 257 MET cc_start: 0.9034 (tpp) cc_final: 0.8758 (tpp) REVERT: D 365 LYS cc_start: 0.9418 (tttt) cc_final: 0.9075 (tttt) REVERT: D 395 LYS cc_start: 0.8523 (mttt) cc_final: 0.8133 (mtmm) REVERT: D 443 LYS cc_start: 0.9521 (mttt) cc_final: 0.9221 (mtmm) REVERT: D 485 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8384 (pp) REVERT: D 494 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8885 (pt) REVERT: D 531 MET cc_start: 0.8744 (pmm) cc_final: 0.8529 (pmm) REVERT: D 532 MET cc_start: 0.9493 (mmm) cc_final: 0.9289 (mmm) REVERT: D 541 MET cc_start: 0.9726 (mmm) cc_final: 0.9443 (mmm) outliers start: 16 outliers final: 4 residues processed: 124 average time/residue: 0.3143 time to fit residues: 57.1180 Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 142 optimal weight: 30.0000 chunk 164 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15121 Z= 0.167 Angle : 0.540 9.240 20604 Z= 0.271 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.536 168.674 2100 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.08 % Allowed : 6.44 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.20), residues: 1863 helix: 2.85 (0.14), residues: 1296 sheet: 2.96 (0.73), residues: 48 loop : -0.38 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 264 HIS 0.003 0.001 HIS D 308 PHE 0.009 0.001 PHE D 270 TYR 0.009 0.001 TYR A 168 ARG 0.003 0.000 ARG C 420 *********************** 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 : 1.535 Fit side-chains REVERT: A 100 MET cc_start: 0.9036 (mmp) cc_final: 0.8429 (mmm) REVERT: A 257 MET cc_start: 0.9034 (tpp) cc_final: 0.8753 (tpp) REVERT: A 365 LYS cc_start: 0.9410 (tttt) cc_final: 0.9129 (tttt) REVERT: A 395 LYS cc_start: 0.8539 (mttt) cc_final: 0.8149 (mtmm) REVERT: A 443 LYS cc_start: 0.9518 (mttt) cc_final: 0.9217 (mtmm) REVERT: A 465 MET cc_start: 0.8889 (ttt) cc_final: 0.8382 (tmm) REVERT: A 485 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8062 (pp) REVERT: A 494 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8742 (pt) REVERT: A 532 MET cc_start: 0.9503 (mmm) cc_final: 0.9293 (mmm) REVERT: A 541 MET cc_start: 0.9727 (mmm) cc_final: 0.9440 (mmm) REVERT: B 100 MET cc_start: 0.9028 (mmp) cc_final: 0.8423 (mmm) REVERT: B 257 MET cc_start: 0.9033 (tpp) cc_final: 0.8751 (tpp) REVERT: B 365 LYS cc_start: 0.9411 (tttt) cc_final: 0.9131 (tttt) REVERT: B 395 LYS cc_start: 0.8540 (mttt) cc_final: 0.8146 (mtmm) REVERT: B 443 LYS cc_start: 0.9522 (mttt) cc_final: 0.9222 (mtmm) REVERT: B 465 MET cc_start: 0.8909 (ttt) cc_final: 0.8684 (ttp) REVERT: B 485 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8411 (pp) REVERT: B 494 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8742 (pt) REVERT: B 532 MET cc_start: 0.9502 (mmm) cc_final: 0.9291 (mmm) REVERT: B 541 MET cc_start: 0.9726 (mmm) cc_final: 0.9443 (mmm) REVERT: C 100 MET cc_start: 0.9029 (mmp) cc_final: 0.8422 (mmm) REVERT: C 257 MET cc_start: 0.9033 (tpp) cc_final: 0.8754 (tpp) REVERT: C 365 LYS cc_start: 0.9410 (tttt) cc_final: 0.9132 (tttt) REVERT: C 395 LYS cc_start: 0.8541 (mttt) cc_final: 0.8148 (mtmm) REVERT: C 443 LYS cc_start: 0.9519 (mttt) cc_final: 0.9218 (mtmm) REVERT: C 465 MET cc_start: 0.8908 (ttt) cc_final: 0.8685 (ttp) REVERT: C 485 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8366 (pp) REVERT: C 494 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8745 (pt) REVERT: C 532 MET cc_start: 0.9505 (mmm) cc_final: 0.9290 (mmm) REVERT: C 541 MET cc_start: 0.9727 (mmm) cc_final: 0.9445 (mmm) REVERT: D 100 MET cc_start: 0.9027 (mmp) cc_final: 0.8420 (mmm) REVERT: D 257 MET cc_start: 0.9033 (tpp) cc_final: 0.8752 (tpp) REVERT: D 365 LYS cc_start: 0.9412 (tttt) cc_final: 0.9132 (tttt) REVERT: D 395 LYS cc_start: 0.8534 (mttt) cc_final: 0.8143 (mtmm) REVERT: D 443 LYS cc_start: 0.9520 (mttt) cc_final: 0.9221 (mtmm) REVERT: D 465 MET cc_start: 0.8909 (ttt) cc_final: 0.8686 (ttp) REVERT: D 485 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8363 (pp) REVERT: D 494 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8742 (pt) REVERT: D 532 MET cc_start: 0.9502 (mmm) cc_final: 0.9288 (mmm) REVERT: D 541 MET cc_start: 0.9725 (mmm) cc_final: 0.9443 (mmm) outliers start: 16 outliers final: 4 residues processed: 124 average time/residue: 0.3082 time to fit residues: 55.2615 Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 chunk 101 optimal weight: 0.0270 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15121 Z= 0.153 Angle : 0.550 9.683 20604 Z= 0.272 Chirality : 0.038 0.117 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.550 168.692 2100 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.81 % Allowed : 7.53 % 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: 3.09 (0.20), residues: 1863 helix: 2.89 (0.14), residues: 1296 sheet: 2.98 (0.73), residues: 48 loop : -0.33 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.002 0.001 HIS C 239 PHE 0.009 0.001 PHE D 270 TYR 0.007 0.001 TYR A 364 ARG 0.003 0.000 ARG D 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.728 Fit side-chains REVERT: A 100 MET cc_start: 0.9036 (mmp) cc_final: 0.8436 (mmm) REVERT: A 257 MET cc_start: 0.9020 (tpp) cc_final: 0.8740 (tpp) REVERT: A 365 LYS cc_start: 0.9411 (tttt) cc_final: 0.9062 (tttt) REVERT: A 395 LYS cc_start: 0.8493 (mttt) cc_final: 0.8118 (mtmm) REVERT: A 443 LYS cc_start: 0.9505 (mttt) cc_final: 0.9205 (mtmm) REVERT: A 465 MET cc_start: 0.8935 (ttt) cc_final: 0.8506 (tmm) REVERT: A 485 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8133 (pp) REVERT: A 494 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8679 (pt) REVERT: A 541 MET cc_start: 0.9724 (mmm) cc_final: 0.9437 (mmm) REVERT: B 100 MET cc_start: 0.9028 (mmp) cc_final: 0.8426 (mmm) REVERT: B 257 MET cc_start: 0.9019 (tpp) cc_final: 0.8740 (tpp) REVERT: B 365 LYS cc_start: 0.9413 (tttt) cc_final: 0.9178 (tttt) REVERT: B 395 LYS cc_start: 0.8491 (mttt) cc_final: 0.8114 (mtmm) REVERT: B 443 LYS cc_start: 0.9509 (mttt) cc_final: 0.9210 (mtmm) REVERT: B 485 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8371 (pp) REVERT: B 494 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8675 (pt) REVERT: B 541 MET cc_start: 0.9723 (mmm) cc_final: 0.9435 (mmm) REVERT: C 100 MET cc_start: 0.9029 (mmp) cc_final: 0.8427 (mmm) REVERT: C 257 MET cc_start: 0.9019 (tpp) cc_final: 0.8739 (tpp) REVERT: C 365 LYS cc_start: 0.9411 (tttt) cc_final: 0.9064 (tttt) REVERT: C 395 LYS cc_start: 0.8494 (mttt) cc_final: 0.8116 (mtmm) REVERT: C 443 LYS cc_start: 0.9518 (mttt) cc_final: 0.9222 (mtmm) REVERT: C 465 MET cc_start: 0.8950 (ttt) cc_final: 0.8512 (tmm) REVERT: C 485 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8370 (pp) REVERT: C 494 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8676 (pt) REVERT: C 541 MET cc_start: 0.9724 (mmm) cc_final: 0.9436 (mmm) REVERT: D 100 MET cc_start: 0.9027 (mmp) cc_final: 0.8425 (mmm) REVERT: D 257 MET cc_start: 0.9019 (tpp) cc_final: 0.8740 (tpp) REVERT: D 365 LYS cc_start: 0.9413 (tttt) cc_final: 0.9064 (tttt) REVERT: D 395 LYS cc_start: 0.8486 (mttt) cc_final: 0.8111 (mtmm) REVERT: D 443 LYS cc_start: 0.9520 (mttt) cc_final: 0.9225 (mtmm) REVERT: D 465 MET cc_start: 0.8951 (ttt) cc_final: 0.8510 (tmm) REVERT: D 485 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8368 (pp) REVERT: D 494 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8674 (pt) REVERT: D 541 MET cc_start: 0.9722 (mmm) cc_final: 0.9434 (mmm) outliers start: 12 outliers final: 4 residues processed: 125 average time/residue: 0.3258 time to fit residues: 58.7597 Evaluate side-chains 120 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 118 optimal weight: 0.3980 chunk 158 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15121 Z= 0.146 Angle : 0.560 10.295 20604 Z= 0.273 Chirality : 0.038 0.120 2378 Planarity : 0.003 0.044 2540 Dihedral : 12.551 169.345 2100 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.81 % Allowed : 7.73 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.15 (0.20), residues: 1863 helix: 2.93 (0.14), residues: 1296 sheet: 2.98 (0.73), residues: 48 loop : -0.28 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.003 0.000 HIS C 308 PHE 0.009 0.001 PHE D 270 TYR 0.006 0.001 TYR A 364 ARG 0.016 0.000 ARG A 534 ********************** 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 130 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9011 (mmp) cc_final: 0.8398 (mmm) REVERT: A 257 MET cc_start: 0.9000 (tpp) cc_final: 0.8722 (tpp) REVERT: A 365 LYS cc_start: 0.9409 (tttt) cc_final: 0.9174 (tttt) REVERT: A 395 LYS cc_start: 0.8437 (mttt) cc_final: 0.8164 (mtmm) REVERT: A 465 MET cc_start: 0.8874 (ttt) cc_final: 0.8568 (tmm) REVERT: A 485 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8026 (pp) REVERT: A 494 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8581 (pt) REVERT: A 541 MET cc_start: 0.9720 (mmm) cc_final: 0.9423 (mmm) REVERT: B 100 MET cc_start: 0.9005 (mmp) cc_final: 0.8390 (mmm) REVERT: B 257 MET cc_start: 0.9000 (tpp) cc_final: 0.8721 (tpp) REVERT: B 365 LYS cc_start: 0.9409 (tttt) cc_final: 0.9174 (tttt) REVERT: B 395 LYS cc_start: 0.8434 (mttt) cc_final: 0.8162 (mtmm) REVERT: B 485 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8428 (pp) REVERT: B 494 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8637 (pt) REVERT: B 541 MET cc_start: 0.9717 (mmm) cc_final: 0.9421 (mmm) REVERT: C 100 MET cc_start: 0.9006 (mmp) cc_final: 0.8392 (mmm) REVERT: C 257 MET cc_start: 0.9005 (tpp) cc_final: 0.8728 (tpp) REVERT: C 365 LYS cc_start: 0.9409 (tttt) cc_final: 0.9176 (tttt) REVERT: C 395 LYS cc_start: 0.8435 (mttt) cc_final: 0.8163 (mtmm) REVERT: C 465 MET cc_start: 0.8934 (ttt) cc_final: 0.8582 (tmm) REVERT: C 485 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8346 (pp) REVERT: C 494 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8561 (pt) REVERT: C 541 MET cc_start: 0.9718 (mmm) cc_final: 0.9423 (mmm) REVERT: D 100 MET cc_start: 0.9003 (mmp) cc_final: 0.8389 (mmm) REVERT: D 257 MET cc_start: 0.9005 (tpp) cc_final: 0.8727 (tpp) REVERT: D 365 LYS cc_start: 0.9410 (tttt) cc_final: 0.9176 (tttt) REVERT: D 395 LYS cc_start: 0.8428 (mttt) cc_final: 0.8160 (mtmm) REVERT: D 465 MET cc_start: 0.8936 (ttt) cc_final: 0.8580 (tmm) REVERT: D 485 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8343 (pp) REVERT: D 494 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8559 (pt) REVERT: D 541 MET cc_start: 0.9717 (mmm) cc_final: 0.9420 (mmm) outliers start: 12 outliers final: 4 residues processed: 130 average time/residue: 0.3319 time to fit residues: 61.6756 Evaluate side-chains 123 residues out of total 1699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 145 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 145 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain D residue 145 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.065545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.048021 restraints weight = 63418.397| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.85 r_work: 0.2766 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15121 Z= 0.152 Angle : 0.571 10.092 20604 Z= 0.278 Chirality : 0.038 0.125 2378 Planarity : 0.003 0.043 2540 Dihedral : 12.547 168.716 2100 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.81 % Allowed : 7.12 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.13 (0.20), residues: 1863 helix: 2.90 (0.14), residues: 1296 sheet: 2.89 (0.71), residues: 48 loop : -0.26 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.000 HIS C 308 PHE 0.009 0.001 PHE D 270 TYR 0.006 0.001 TYR A 364 ARG 0.015 0.000 ARG C 534 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2541.98 seconds wall clock time: 48 minutes 24.85 seconds (2904.85 seconds total)