Starting phenix.real_space_refine on Fri Jul 3 18:08:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cc2_45432/07_2026/9cc2_45432.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cc2_45432/07_2026/9cc2_45432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cc2_45432/07_2026/9cc2_45432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cc2_45432/07_2026/9cc2_45432.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cc2_45432/07_2026/9cc2_45432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cc2_45432/07_2026/9cc2_45432.map" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 16 5.49 5 S 96 5.16 5 C 10212 2.51 5 N 2512 2.21 5 O 2720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15556 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3758 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 2 Chain: "B" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3758 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 2 Chain: "C" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3758 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 2 Chain: "D" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3758 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 13, 'TRANS': 450} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'FO4': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'FO4': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'FO4': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'FO4': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.68, per 1000 atoms: 0.24 Number of scatterers: 15556 At special positions: 0 Unit cell: (110.39, 110.39, 110.39, 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 96 16.00 P 16 15.00 O 2720 8.00 N 2512 7.00 C 10212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.03 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 676.0 milliseconds 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3512 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 67.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 63 through 106 removed outlier: 3.516A pdb=" N MET A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 138 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 297 through 338 removed outlier: 3.572A pdb=" N ARG A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.661A pdb=" N ARG A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 377 Processing helix chain 'A' and resid 382 through 406 removed outlier: 4.133A pdb=" N CYS A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 448 removed outlier: 4.112A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Proline residue: A 423 - end of helix removed outlier: 4.041A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.860A pdb=" N ARG A 455 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.671A pdb=" N THR A 476 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 508 Processing helix chain 'A' and resid 508 through 526 Processing helix chain 'B' and resid 40 through 48 Processing helix chain 'B' and resid 51 through 60 Processing helix chain 'B' and resid 63 through 106 removed outlier: 3.515A pdb=" N MET B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 138 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 297 through 338 removed outlier: 3.572A pdb=" N ARG B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 removed outlier: 3.660A pdb=" N ARG B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 382 through 406 removed outlier: 4.133A pdb=" N CYS B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 448 removed outlier: 4.113A pdb=" N LEU B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 4.041A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.861A pdb=" N ARG B 455 " --> pdb=" O VAL B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.671A pdb=" N THR B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 508 Processing helix chain 'B' and resid 508 through 526 Processing helix chain 'C' and resid 40 through 48 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 63 through 106 removed outlier: 3.515A pdb=" N MET C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 138 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 297 through 338 removed outlier: 3.572A pdb=" N ARG C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.660A pdb=" N ARG C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 377 Processing helix chain 'C' and resid 382 through 406 removed outlier: 4.132A pdb=" N CYS C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 448 removed outlier: 4.113A pdb=" N LEU C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Proline residue: C 423 - end of helix removed outlier: 4.041A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.861A pdb=" N ARG C 455 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 469 Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.671A pdb=" N THR C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 508 Processing helix chain 'C' and resid 508 through 526 Processing helix chain 'D' and resid 40 through 48 Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 63 through 106 removed outlier: 3.516A pdb=" N MET D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 138 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 297 through 338 removed outlier: 3.572A pdb=" N ARG D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 350 removed outlier: 3.660A pdb=" N ARG D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 377 Processing helix chain 'D' and resid 382 through 406 removed outlier: 4.132A pdb=" N CYS D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 448 removed outlier: 4.114A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Proline residue: D 423 - end of helix removed outlier: 4.041A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 3.862A pdb=" N ARG D 455 " --> pdb=" O VAL D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.671A pdb=" N THR D 476 " --> pdb=" O ASP D 472 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 508 Processing helix chain 'D' and resid 508 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 6.801A pdb=" N ARG A 168 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 231 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS A 166 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 233 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 164 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG A 187 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY A 173 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASP A 185 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL A 175 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASP A 183 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA3, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.801A pdb=" N ARG B 168 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 231 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS B 166 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B 233 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 164 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG B 187 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY B 173 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ASP B 185 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL B 175 " --> pdb=" O ASP B 183 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASP B 183 " --> pdb=" O VAL B 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 119 removed outlier: 6.801A pdb=" N ARG C 168 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 231 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS C 166 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE C 233 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA C 164 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG C 187 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY C 173 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASP C 185 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL C 175 " --> pdb=" O ASP C 183 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASP C 183 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 149 Processing sheet with id=AA7, first strand: chain 'D' and resid 118 through 119 removed outlier: 6.801A pdb=" N ARG D 168 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL D 231 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS D 166 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE D 233 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA D 164 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ARG D 187 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLY D 173 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ASP D 185 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL D 175 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ASP D 183 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 149 1097 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2284 1.31 - 1.44: 4573 1.44 - 1.56: 8903 1.56 - 1.69: 24 1.69 - 1.81: 132 Bond restraints: 15916 Sorted by residual: bond pdb=" C1B PIO D 602 " pdb=" O3C PIO D 602 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1B PIO C 602 " pdb=" O3C PIO C 602 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1B PIO A 601 " pdb=" O3C PIO A 601 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1B PIO B 602 " pdb=" O3C PIO B 602 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1A PIO C 602 " pdb=" O2C PIO C 602 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 15911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 21321 2.37 - 4.73: 151 4.73 - 7.10: 44 7.10 - 9.47: 16 9.47 - 11.83: 8 Bond angle restraints: 21540 Sorted by residual: angle pdb=" O11 PIO C 602 " pdb=" P1 PIO C 602 " pdb=" O12 PIO C 602 " ideal model delta sigma weight residual 121.09 109.26 11.83 3.00e+00 1.11e-01 1.56e+01 angle pdb=" O11 PIO D 602 " pdb=" P1 PIO D 602 " pdb=" O12 PIO D 602 " ideal model delta sigma weight residual 121.09 109.26 11.83 3.00e+00 1.11e-01 1.56e+01 angle pdb=" O11 PIO A 601 " pdb=" P1 PIO A 601 " pdb=" O12 PIO A 601 " ideal model delta sigma weight residual 121.09 109.29 11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 PIO B 602 " pdb=" P1 PIO B 602 " pdb=" O12 PIO B 602 " ideal model delta sigma weight residual 121.09 109.30 11.79 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O1 PIO C 602 " pdb=" P1 PIO C 602 " pdb=" O13 PIO C 602 " ideal model delta sigma weight residual 97.64 108.64 -11.00 3.00e+00 1.11e-01 1.35e+01 ... (remaining 21535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.04: 8690 26.04 - 52.08: 666 52.08 - 78.12: 84 78.12 - 104.15: 16 104.15 - 130.19: 12 Dihedral angle restraints: 9468 sinusoidal: 4020 harmonic: 5448 Sorted by residual: dihedral pdb=" C31 FO4 D 601 " pdb=" C32 FO4 D 601 " pdb=" C33 FO4 D 601 " pdb=" C34 FO4 D 601 " ideal model delta sinusoidal sigma weight residual 97.16 -132.65 -130.19 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C31 FO4 A 602 " pdb=" C32 FO4 A 602 " pdb=" C33 FO4 A 602 " pdb=" C34 FO4 A 602 " ideal model delta sinusoidal sigma weight residual 97.16 -132.65 -130.19 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C31 FO4 C 601 " pdb=" C32 FO4 C 601 " pdb=" C33 FO4 C 601 " pdb=" C34 FO4 C 601 " ideal model delta sinusoidal sigma weight residual 97.16 -132.67 -130.17 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 9465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1551 0.027 - 0.055: 563 0.055 - 0.082: 220 0.082 - 0.109: 109 0.109 - 0.137: 33 Chirality restraints: 2476 Sorted by residual: chirality pdb=" C1 PIO C 602 " pdb=" C2 PIO C 602 " pdb=" C6 PIO C 602 " pdb=" O1 PIO C 602 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" C1 PIO B 602 " pdb=" C2 PIO B 602 " pdb=" C6 PIO B 602 " pdb=" O1 PIO B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" C1 PIO A 601 " pdb=" C2 PIO A 601 " pdb=" C6 PIO A 601 " pdb=" O1 PIO A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 2473 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 448 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO A 449 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 448 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.99e+00 pdb=" N PRO D 449 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 449 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 449 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 448 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 449 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " 0.020 5.00e-02 4.00e+02 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1657 2.75 - 3.29: 15045 3.29 - 3.82: 26898 3.82 - 4.36: 31113 4.36 - 4.90: 53483 Nonbonded interactions: 128196 Sorted by model distance: nonbonded pdb=" OD1 ASP B 134 " pdb=" OH TYR B 218 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASP A 134 " pdb=" OH TYR A 218 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASP C 134 " pdb=" OH TYR C 218 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP D 134 " pdb=" OH TYR D 218 " model vdw 2.212 3.040 nonbonded pdb=" O ARG B 403 " pdb=" OG1 THR B 406 " model vdw 2.316 3.040 ... (remaining 128191 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 527) selection = (chain 'B' and resid 39 through 527) selection = (chain 'C' and resid 39 through 527) selection = (chain 'D' and resid 39 through 527) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.580 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 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 : 0.003 0.068 15928 Z= 0.170 Angle : 0.631 11.833 21572 Z= 0.282 Chirality : 0.038 0.137 2476 Planarity : 0.003 0.035 2596 Dihedral : 18.215 130.193 5944 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 19.88 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.20), residues: 1832 helix: 3.21 (0.15), residues: 1112 sheet: 1.26 (0.37), residues: 252 loop : -0.57 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 151 TYR 0.013 0.001 TYR B 497 PHE 0.008 0.001 PHE A 235 TRP 0.010 0.001 TRP A 398 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (15916) covalent geometry : angle 0.62889 / 0.28 (21540) SS BOND : bond 0.00320 / 0.16 ( 4) SS BOND : angle 0.94658 / 0.45 ( 8) hydrogen bonds : bond 0.12197 / 8.08 ( 1057) hydrogen bonds : angle 5.92958 / 4.21 ( 3183) link_BETA1-4 : bond 0.00225 / 0.11 ( 4) link_BETA1-4 : angle 2.29582 / 1.20 ( 12) link_NAG-ASN : bond 0.00063 / 0.03 ( 4) link_NAG-ASN : angle 0.96630 / 0.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.606 Fit side-chains REVERT: A 67 MET cc_start: 0.7878 (mmt) cc_final: 0.7624 (mmm) REVERT: B 67 MET cc_start: 0.7863 (mmt) cc_final: 0.7613 (mmm) REVERT: C 67 MET cc_start: 0.7889 (mmt) cc_final: 0.7588 (mmm) REVERT: D 67 MET cc_start: 0.7868 (mmt) cc_final: 0.7619 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.4536 time to fit residues: 39.3741 Evaluate side-chains 72 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS D 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.065826 restraints weight = 25061.758| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.20 r_work: 0.2720 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.0519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 15928 Z= 0.129 Angle : 0.473 5.692 21572 Z= 0.254 Chirality : 0.039 0.132 2476 Planarity : 0.003 0.035 2596 Dihedral : 11.780 130.655 2484 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.99 % Allowed : 18.07 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.20), residues: 1832 helix: 3.16 (0.15), residues: 1116 sheet: 1.37 (0.36), residues: 200 loop : -0.49 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 168 TYR 0.012 0.001 TYR A 497 PHE 0.014 0.001 PHE C 235 TRP 0.009 0.001 TRP A 398 HIS 0.004 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (15916) covalent geometry : angle 0.46925 / 0.25 (21540) SS BOND : bond 0.00466 / 0.23 ( 4) SS BOND : angle 0.95579 / 0.46 ( 8) hydrogen bonds : bond 0.05294 / 3.53 ( 1057) hydrogen bonds : angle 4.71596 / 3.36 ( 3183) link_BETA1-4 : bond 0.00204 / 0.10 ( 4) link_BETA1-4 : angle 2.24676 / 1.19 ( 12) link_NAG-ASN : bond 0.00096 / 0.05 ( 4) link_NAG-ASN : angle 1.21753 / 0.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.673 Fit side-chains REVERT: A 67 MET cc_start: 0.7770 (mmt) cc_final: 0.7509 (mmm) REVERT: A 376 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: B 67 MET cc_start: 0.7765 (mmt) cc_final: 0.7503 (mmm) REVERT: B 376 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: C 67 MET cc_start: 0.7774 (mmt) cc_final: 0.7511 (mmm) REVERT: C 376 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: D 67 MET cc_start: 0.7767 (mmt) cc_final: 0.7505 (mmm) REVERT: D 376 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7688 (mt-10) outliers start: 33 outliers final: 8 residues processed: 105 average time/residue: 0.4445 time to fit residues: 53.6646 Evaluate side-chains 82 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 376 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 45 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.063192 restraints weight = 25288.474| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.17 r_work: 0.2663 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9236 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15928 Z= 0.232 Angle : 0.543 7.238 21572 Z= 0.288 Chirality : 0.043 0.148 2476 Planarity : 0.004 0.036 2596 Dihedral : 12.240 130.260 2484 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.99 % Allowed : 18.13 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.19), residues: 1832 helix: 2.93 (0.14), residues: 1116 sheet: 1.35 (0.33), residues: 204 loop : -0.65 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 270 TYR 0.012 0.002 TYR A 497 PHE 0.018 0.001 PHE D 235 TRP 0.012 0.001 TRP B 398 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.23 (15916) covalent geometry : angle 0.53716 / 0.29 (21540) SS BOND : bond 0.00499 / 0.25 ( 4) SS BOND : angle 1.19917 / 0.59 ( 8) hydrogen bonds : bond 0.06502 / 4.35 ( 1057) hydrogen bonds : angle 4.85175 / 3.45 ( 3183) link_BETA1-4 : bond 0.00095 / 0.05 ( 4) link_BETA1-4 : angle 2.83419 / 1.52 ( 12) link_NAG-ASN : bond 0.00230 / 0.12 ( 4) link_NAG-ASN : angle 1.69512 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.645 Fit side-chains REVERT: A 67 MET cc_start: 0.7934 (mmt) cc_final: 0.7694 (mmm) REVERT: B 67 MET cc_start: 0.7895 (mmt) cc_final: 0.7654 (mmm) REVERT: C 67 MET cc_start: 0.7916 (mmt) cc_final: 0.7631 (mmm) REVERT: D 67 MET cc_start: 0.7920 (mmt) cc_final: 0.7677 (mmm) outliers start: 33 outliers final: 12 residues processed: 98 average time/residue: 0.5060 time to fit residues: 56.1844 Evaluate side-chains 85 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 158 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.066873 restraints weight = 25276.175| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.20 r_work: 0.2742 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.0741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15928 Z= 0.108 Angle : 0.451 5.931 21572 Z= 0.241 Chirality : 0.039 0.159 2476 Planarity : 0.003 0.037 2596 Dihedral : 11.662 130.482 2484 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.90 % Allowed : 18.80 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.09 (0.20), residues: 1832 helix: 3.21 (0.15), residues: 1120 sheet: 1.61 (0.34), residues: 204 loop : -0.59 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 274 TYR 0.012 0.001 TYR C 497 PHE 0.012 0.001 PHE B 333 TRP 0.009 0.001 TRP B 398 HIS 0.003 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (15916) covalent geometry : angle 0.44676 / 0.24 (21540) SS BOND : bond 0.00552 / 0.28 ( 4) SS BOND : angle 1.35731 / 0.64 ( 8) hydrogen bonds : bond 0.04789 / 3.21 ( 1057) hydrogen bonds : angle 4.42595 / 3.16 ( 3183) link_BETA1-4 : bond 0.00233 / 0.12 ( 4) link_BETA1-4 : angle 2.14111 / 1.12 ( 12) link_NAG-ASN : bond 0.00034 / 0.02 ( 4) link_NAG-ASN : angle 0.87613 / 0.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.567 Fit side-chains REVERT: A 67 MET cc_start: 0.7775 (mmt) cc_final: 0.7549 (mmm) REVERT: B 67 MET cc_start: 0.7750 (mmt) cc_final: 0.7527 (mmm) REVERT: C 67 MET cc_start: 0.7760 (mmt) cc_final: 0.7525 (mmm) REVERT: D 67 MET cc_start: 0.7783 (mmt) cc_final: 0.7554 (mmm) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.5110 time to fit residues: 50.3127 Evaluate side-chains 81 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 153 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.062762 restraints weight = 25426.493| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.19 r_work: 0.2652 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9241 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15928 Z= 0.255 Angle : 0.564 7.234 21572 Z= 0.297 Chirality : 0.045 0.145 2476 Planarity : 0.004 0.036 2596 Dihedral : 12.174 129.905 2484 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.81 % Allowed : 18.07 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.19), residues: 1832 helix: 2.90 (0.14), residues: 1116 sheet: 1.30 (0.33), residues: 204 loop : -0.70 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 270 TYR 0.012 0.002 TYR A 497 PHE 0.019 0.002 PHE C 235 TRP 0.012 0.002 TRP B 398 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.25 (15916) covalent geometry : angle 0.55737 / 0.30 (21540) SS BOND : bond 0.00646 / 0.32 ( 4) SS BOND : angle 1.62590 / 0.79 ( 8) hydrogen bonds : bond 0.06709 / 4.49 ( 1057) hydrogen bonds : angle 4.82526 / 3.43 ( 3183) link_BETA1-4 : bond 0.00094 / 0.05 ( 4) link_BETA1-4 : angle 3.01595 / 1.63 ( 12) link_NAG-ASN : bond 0.00293 / 0.15 ( 4) link_NAG-ASN : angle 1.82639 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.449 Fit side-chains REVERT: A 67 MET cc_start: 0.7912 (mmt) cc_final: 0.7684 (mmm) REVERT: B 67 MET cc_start: 0.7906 (mmt) cc_final: 0.7648 (mmm) REVERT: C 67 MET cc_start: 0.7901 (mmt) cc_final: 0.7647 (mmm) outliers start: 30 outliers final: 12 residues processed: 95 average time/residue: 0.5112 time to fit residues: 54.7641 Evaluate side-chains 82 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 101 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 182 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.101503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.064948 restraints weight = 25010.099| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.19 r_work: 0.2700 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 15928 Z= 0.129 Angle : 0.479 6.582 21572 Z= 0.255 Chirality : 0.039 0.155 2476 Planarity : 0.003 0.036 2596 Dihedral : 11.901 129.740 2484 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.33 % Allowed : 18.67 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.19), residues: 1832 helix: 3.12 (0.15), residues: 1116 sheet: 1.44 (0.34), residues: 204 loop : -0.73 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 337 TYR 0.013 0.001 TYR C 497 PHE 0.013 0.001 PHE B 235 TRP 0.011 0.001 TRP B 398 HIS 0.004 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (15916) covalent geometry : angle 0.47413 / 0.25 (21540) SS BOND : bond 0.00436 / 0.22 ( 4) SS BOND : angle 0.90564 / 0.44 ( 8) hydrogen bonds : bond 0.05432 / 3.64 ( 1057) hydrogen bonds : angle 4.53957 / 3.23 ( 3183) link_BETA1-4 : bond 0.00162 / 0.08 ( 4) link_BETA1-4 : angle 2.43334 / 1.28 ( 12) link_NAG-ASN : bond 0.00044 / 0.02 ( 4) link_NAG-ASN : angle 1.28576 / 0.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.600 Fit side-chains REVERT: B 67 MET cc_start: 0.7828 (mmt) cc_final: 0.7583 (mmm) REVERT: C 67 MET cc_start: 0.7830 (mmt) cc_final: 0.7580 (mmm) outliers start: 22 outliers final: 13 residues processed: 107 average time/residue: 0.4485 time to fit residues: 54.8831 Evaluate side-chains 93 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 44 optimal weight: 0.7980 chunk 152 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 HIS B 409 HIS C 409 HIS D 409 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.064721 restraints weight = 25022.262| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.17 r_work: 0.2692 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9215 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15928 Z= 0.149 Angle : 0.489 6.765 21572 Z= 0.260 Chirality : 0.040 0.152 2476 Planarity : 0.003 0.035 2596 Dihedral : 11.836 129.316 2484 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.02 % Allowed : 19.46 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.19), residues: 1832 helix: 3.11 (0.15), residues: 1116 sheet: 1.44 (0.34), residues: 204 loop : -0.73 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.013 0.001 TYR B 497 PHE 0.014 0.001 PHE C 235 TRP 0.010 0.001 TRP B 398 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15916) covalent geometry : angle 0.48401 / 0.26 (21540) SS BOND : bond 0.00406 / 0.20 ( 4) SS BOND : angle 0.94605 / 0.46 ( 8) hydrogen bonds : bond 0.05567 / 3.73 ( 1057) hydrogen bonds : angle 4.53956 / 3.23 ( 3183) link_BETA1-4 : bond 0.00182 / 0.09 ( 4) link_BETA1-4 : angle 2.52659 / 1.35 ( 12) link_NAG-ASN : bond 0.00091 / 0.05 ( 4) link_NAG-ASN : angle 1.34347 / 0.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.606 Fit side-chains REVERT: B 67 MET cc_start: 0.7822 (mmt) cc_final: 0.7594 (mmm) REVERT: C 67 MET cc_start: 0.7819 (mmt) cc_final: 0.7575 (mmm) outliers start: 17 outliers final: 13 residues processed: 102 average time/residue: 0.4381 time to fit residues: 51.1112 Evaluate side-chains 90 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 HIS B 409 HIS C 409 HIS D 409 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.064504 restraints weight = 25166.319| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.18 r_work: 0.2689 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9214 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15928 Z= 0.156 Angle : 0.495 6.715 21572 Z= 0.263 Chirality : 0.041 0.152 2476 Planarity : 0.003 0.035 2596 Dihedral : 11.794 128.740 2484 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.27 % Allowed : 19.82 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.19), residues: 1832 helix: 3.10 (0.14), residues: 1116 sheet: 1.41 (0.34), residues: 204 loop : -0.78 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.013 0.001 TYR B 497 PHE 0.014 0.001 PHE C 235 TRP 0.011 0.001 TRP B 398 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (15916) covalent geometry : angle 0.48980 / 0.26 (21540) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 0.93288 / 0.46 ( 8) hydrogen bonds : bond 0.05662 / 3.79 ( 1057) hydrogen bonds : angle 4.54538 / 3.23 ( 3183) link_BETA1-4 : bond 0.00193 / 0.10 ( 4) link_BETA1-4 : angle 2.55752 / 1.36 ( 12) link_NAG-ASN : bond 0.00099 / 0.05 ( 4) link_NAG-ASN : angle 1.41851 / 0.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.551 Fit side-chains REVERT: A 285 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6734 (pptt) REVERT: D 343 SER cc_start: 0.7890 (OUTLIER) cc_final: 0.7583 (p) outliers start: 21 outliers final: 15 residues processed: 100 average time/residue: 0.4277 time to fit residues: 48.7980 Evaluate side-chains 95 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 133 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 HIS B 409 HIS C 409 HIS D 409 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.063235 restraints weight = 25249.816| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.18 r_work: 0.2659 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9244 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15928 Z= 0.218 Angle : 0.543 7.308 21572 Z= 0.287 Chirality : 0.043 0.148 2476 Planarity : 0.004 0.035 2596 Dihedral : 11.937 127.503 2484 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.33 % Allowed : 19.64 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.19), residues: 1832 helix: 2.95 (0.14), residues: 1116 sheet: 1.16 (0.33), residues: 204 loop : -0.80 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.013 0.002 TYR C 47 PHE 0.018 0.001 PHE D 235 TRP 0.012 0.001 TRP B 398 HIS 0.004 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (15916) covalent geometry : angle 0.53744 / 0.29 (21540) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 1.28615 / 0.64 ( 8) hydrogen bonds : bond 0.06368 / 4.26 ( 1057) hydrogen bonds : angle 4.70178 / 3.33 ( 3183) link_BETA1-4 : bond 0.00109 / 0.05 ( 4) link_BETA1-4 : angle 2.87891 / 1.55 ( 12) link_NAG-ASN : bond 0.00206 / 0.10 ( 4) link_NAG-ASN : angle 1.75049 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.487 Fit side-chains REVERT: A 285 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6679 (pptt) REVERT: B 285 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6676 (pptt) REVERT: D 343 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7564 (p) outliers start: 22 outliers final: 16 residues processed: 97 average time/residue: 0.4406 time to fit residues: 48.4658 Evaluate side-chains 97 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 123 optimal weight: 0.1980 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 HIS B 409 HIS D 409 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.101526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065242 restraints weight = 25120.019| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.18 r_work: 0.2706 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15928 Z= 0.133 Angle : 0.481 6.362 21572 Z= 0.256 Chirality : 0.040 0.156 2476 Planarity : 0.003 0.035 2596 Dihedral : 11.693 126.685 2484 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.14 % Allowed : 20.06 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.19), residues: 1832 helix: 3.16 (0.15), residues: 1116 sheet: 1.31 (0.34), residues: 204 loop : -0.79 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 337 TYR 0.013 0.001 TYR C 497 PHE 0.013 0.001 PHE C 235 TRP 0.011 0.001 TRP D 398 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15916) covalent geometry : angle 0.47689 / 0.26 (21540) SS BOND : bond 0.00335 / 0.17 ( 4) SS BOND : angle 0.84028 / 0.41 ( 8) hydrogen bonds : bond 0.05327 / 3.57 ( 1057) hydrogen bonds : angle 4.45295 / 3.16 ( 3183) link_BETA1-4 : bond 0.00259 / 0.13 ( 4) link_BETA1-4 : angle 2.41603 / 1.27 ( 12) link_NAG-ASN : bond 0.00062 / 0.03 ( 4) link_NAG-ASN : angle 1.20741 / 0.59 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3664 Ramachandran restraints generated. 1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.421 Fit side-chains REVERT: C 343 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7611 (p) REVERT: D 343 SER cc_start: 0.7897 (OUTLIER) cc_final: 0.7594 (p) outliers start: 19 outliers final: 14 residues processed: 103 average time/residue: 0.4223 time to fit residues: 49.2923 Evaluate side-chains 96 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 343 SER Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 343 SER Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 57 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 HIS B 409 HIS C 409 HIS D 409 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.102947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.066614 restraints weight = 25141.174| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.20 r_work: 0.2736 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 15928 Z= 0.115 Angle : 0.456 6.090 21572 Z= 0.243 Chirality : 0.039 0.156 2476 Planarity : 0.003 0.036 2596 Dihedral : 11.408 125.431 2484 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.02 % Allowed : 20.18 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.20), residues: 1832 helix: 3.28 (0.15), residues: 1112 sheet: 1.40 (0.35), residues: 204 loop : -0.81 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.013 0.001 TYR D 47 PHE 0.015 0.001 PHE B 333 TRP 0.009 0.001 TRP C 398 HIS 0.003 0.001 HIS D 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15916) covalent geometry : angle 0.45241 / 0.24 (21540) SS BOND : bond 0.00257 / 0.13 ( 4) SS BOND : angle 0.71014 / 0.35 ( 8) hydrogen bonds : bond 0.04820 / 3.22 ( 1057) hydrogen bonds : angle 4.27185 / 3.03 ( 3183) link_BETA1-4 : bond 0.00290 / 0.15 ( 4) link_BETA1-4 : angle 2.18573 / 1.15 ( 12) link_NAG-ASN : bond 0.00007 / 0.00 ( 4) link_NAG-ASN : angle 0.95621 / 0.48 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4462.92 seconds wall clock time: 77 minutes 7.56 seconds (4627.56 seconds total)