Starting phenix.real_space_refine on Sat Jul 4 22:09:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.cif" model { file = "/net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foz_29357/07_2026/8foz_29357.cif" } resolution = 2.0 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= 0.227 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 24 5.49 5 S 144 5.16 5 C 14832 2.51 5 N 4040 2.21 5 O 4608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.03s 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: 23648 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "B" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "C" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "E" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "F" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "G" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "H" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 4.78, per 1000 atoms: 0.20 Number of scatterers: 23648 At special positions: 0 Unit cell: (122.235, 122.235, 120.549, 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 144 16.00 P 24 15.00 O 4608 8.00 N 4040 7.00 C 14832 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 919.8 milliseconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5520 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 43.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.270A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.534A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.266A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.542A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.268A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.538A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.269A pdb=" N TYR D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.539A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 356 removed outlier: 4.025A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 110 Processing helix chain 'E' and resid 254 through 267 removed outlier: 4.268A pdb=" N TYR E 258 " --> pdb=" O GLU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.535A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.265A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.537A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 254 through 267 removed outlier: 4.267A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.541A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 356 removed outlier: 4.025A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 110 Processing helix chain 'H' and resid 254 through 267 removed outlier: 4.259A pdb=" N TYR H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.533A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 356 removed outlier: 4.026A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 416 through 421 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.175A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.511A pdb=" N ILE A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.659A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.168A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.661A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.177A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.646A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.181A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 4.173A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.658A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.661A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.168A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.645A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 4.174A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.654A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 4.165A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2859 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: 4.17 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3952 1.30 - 1.43: 5962 1.43 - 1.56: 13870 1.56 - 1.69: 40 1.69 - 1.82: 240 Bond restraints: 24064 Sorted by residual: bond pdb=" C5 IMP A 601 " pdb=" C6 IMP A 601 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C5 IMP E 601 " pdb=" C6 IMP E 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP H 601 " pdb=" C6 IMP H 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP G 601 " pdb=" C6 IMP G 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP D 601 " pdb=" C6 IMP D 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 24059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 31072 1.84 - 3.67: 1247 3.67 - 5.51: 182 5.51 - 7.34: 37 7.34 - 9.18: 30 Bond angle restraints: 32568 Sorted by residual: angle pdb=" N GLY G 9 " pdb=" CA GLY G 9 " pdb=" C GLY G 9 " ideal model delta sigma weight residual 110.77 104.64 6.13 1.93e+00 2.68e-01 1.01e+01 angle pdb=" N GLY D 9 " pdb=" CA GLY D 9 " pdb=" C GLY D 9 " ideal model delta sigma weight residual 110.77 104.68 6.09 1.93e+00 2.68e-01 9.97e+00 angle pdb=" N GLY H 9 " pdb=" CA GLY H 9 " pdb=" C GLY H 9 " ideal model delta sigma weight residual 110.77 104.70 6.07 1.93e+00 2.68e-01 9.90e+00 angle pdb=" N GLY A 9 " pdb=" CA GLY A 9 " pdb=" C GLY A 9 " ideal model delta sigma weight residual 110.77 104.76 6.01 1.93e+00 2.68e-01 9.69e+00 angle pdb=" N GLY C 9 " pdb=" CA GLY C 9 " pdb=" C GLY C 9 " ideal model delta sigma weight residual 110.77 104.78 5.99 1.93e+00 2.68e-01 9.64e+00 ... (remaining 32563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 13429 26.09 - 52.18: 701 52.18 - 78.27: 76 78.27 - 104.36: 30 104.36 - 130.45: 4 Dihedral angle restraints: 14240 sinusoidal: 5544 harmonic: 8696 Sorted by residual: dihedral pdb=" C5' IMP H 601 " pdb=" O5' IMP H 601 " pdb=" P IMP H 601 " pdb=" O2P IMP H 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.48 130.45 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" C5' IMP F 601 " pdb=" O5' IMP F 601 " pdb=" P IMP F 601 " pdb=" O2P IMP F 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.65 130.28 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.69 130.24 1 2.00e+01 2.50e-03 3.95e+01 ... (remaining 14237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2735 0.064 - 0.127: 884 0.127 - 0.191: 70 0.191 - 0.254: 15 0.254 - 0.318: 8 Chirality restraints: 3712 Sorted by residual: chirality pdb=" CB VAL E 361 " pdb=" CA VAL E 361 " pdb=" CG1 VAL E 361 " pdb=" CG2 VAL E 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL H 361 " pdb=" CA VAL H 361 " pdb=" CG1 VAL H 361 " pdb=" CG2 VAL H 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB VAL A 361 " pdb=" CA VAL A 361 " pdb=" CG1 VAL A 361 " pdb=" CG2 VAL A 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3709 not shown) Planarity restraints: 4120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 4 " 0.021 2.00e-02 2.50e+03 1.61e-02 5.19e+00 pdb=" CG TYR E 4 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 4 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR E 4 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 4 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 4 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 4 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 4 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 4 " -0.021 2.00e-02 2.50e+03 1.60e-02 5.14e+00 pdb=" CG TYR D 4 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 4 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 4 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 4 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 4 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 4 " -0.021 2.00e-02 2.50e+03 1.60e-02 5.11e+00 pdb=" CG TYR A 4 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 4 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 4 " -0.000 2.00e-02 2.50e+03 ... (remaining 4117 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4508 2.77 - 3.30: 22596 3.30 - 3.84: 41452 3.84 - 4.37: 50664 4.37 - 4.90: 83912 Nonbonded interactions: 203132 Sorted by model distance: nonbonded pdb=" OD1 ASP A 418 " pdb=" NH1 ARG D 512 " model vdw 2.238 3.120 nonbonded pdb=" NH1 ARG G 512 " pdb=" OD1 ASP H 418 " model vdw 2.240 3.120 nonbonded pdb=" NH1 ARG A 512 " pdb=" OD1 ASP B 418 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP E 418 " pdb=" NH1 ARG H 512 " model vdw 2.260 3.120 nonbonded pdb=" NH1 ARG E 512 " pdb=" OD1 ASP F 418 " model vdw 2.268 3.120 ... (remaining 203127 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = 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: 4.850 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.120 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 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:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 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 : 0.009 0.139 24072 Z= 0.420 Angle : 0.919 9.180 32568 Z= 0.483 Chirality : 0.059 0.318 3712 Planarity : 0.005 0.040 4120 Dihedral : 15.664 130.450 8720 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.31 % Allowed : 8.91 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.22 (0.15), residues: 3024 helix: 0.71 (0.14), residues: 1232 sheet: -0.42 (0.24), residues: 384 loop : -0.05 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 412 TYR 0.039 0.004 TYR E 4 PHE 0.019 0.004 PHE G 24 HIS 0.005 0.002 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00891 / 0.42 (24064) covalent geometry : angle 0.91870 / 0.48 (32568) hydrogen bonds : bond 0.13963 / 9.27 ( 1022) hydrogen bonds : angle 6.39720 / 4.42 ( 2859) Misc. bond : bond 0.00046 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 369 time to evaluate : 0.551 Fit side-chains REVERT: D 98 GLU cc_start: 0.8112 (mp0) cc_final: 0.7893 (mp0) REVERT: G 62 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8239 (mttt) REVERT: G 98 GLU cc_start: 0.8114 (mp0) cc_final: 0.7900 (mp0) REVERT: G 437 ILE cc_start: 0.8384 (mm) cc_final: 0.8176 (mp) outliers start: 32 outliers final: 24 residues processed: 397 average time/residue: 0.7650 time to fit residues: 339.0776 Evaluate side-chains 389 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 364 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.121297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.097630 restraints weight = 20103.984| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.19 r_work: 0.2945 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.0623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 24072 Z= 0.168 Angle : 0.592 4.763 32568 Z= 0.333 Chirality : 0.046 0.199 3712 Planarity : 0.004 0.030 4120 Dihedral : 9.832 114.449 3444 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.43 % Allowed : 7.76 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.66 (0.15), residues: 3024 helix: 1.25 (0.15), residues: 1240 sheet: -0.44 (0.23), residues: 384 loop : 0.10 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 407 TYR 0.017 0.002 TYR G 4 PHE 0.013 0.002 PHE D 401 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (24064) covalent geometry : angle 0.59212 / 0.33 (32568) hydrogen bonds : bond 0.06393 / 4.22 ( 1022) hydrogen bonds : angle 5.65613 / 3.90 ( 2859) Misc. bond : bond 0.00006 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 370 time to evaluate : 0.922 Fit side-chains REVERT: A 98 GLU cc_start: 0.8416 (mp0) cc_final: 0.8213 (mp0) REVERT: B 105 ARG cc_start: 0.8459 (ttp80) cc_final: 0.7971 (ttp-110) REVERT: D 98 GLU cc_start: 0.8384 (mp0) cc_final: 0.8091 (mp0) REVERT: D 399 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7569 (tp30) REVERT: E 105 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8019 (ttp-110) REVERT: G 98 GLU cc_start: 0.8396 (mp0) cc_final: 0.8111 (mp0) REVERT: G 105 ARG cc_start: 0.8469 (ttp80) cc_final: 0.7895 (ttp-170) REVERT: H 105 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7945 (ttp-170) outliers start: 35 outliers final: 31 residues processed: 400 average time/residue: 0.7750 time to fit residues: 345.1872 Evaluate side-chains 394 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 363 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 GLN D 21 GLN E 265 GLN F 265 GLN G 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096477 restraints weight = 20143.347| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.19 r_work: 0.2928 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 24072 Z= 0.209 Angle : 0.648 5.267 32568 Z= 0.363 Chirality : 0.049 0.241 3712 Planarity : 0.005 0.033 4120 Dihedral : 9.824 116.249 3440 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.76 % Allowed : 8.17 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.49 (0.15), residues: 3024 helix: 1.08 (0.14), residues: 1240 sheet: -0.51 (0.23), residues: 384 loop : 0.01 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 341 TYR 0.018 0.002 TYR B 4 PHE 0.015 0.003 PHE D 401 HIS 0.005 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (24064) covalent geometry : angle 0.64770 / 0.36 (32568) hydrogen bonds : bond 0.07076 / 4.67 ( 1022) hydrogen bonds : angle 5.76956 / 3.99 ( 2859) Misc. bond : bond 0.00012 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 388 time to evaluate : 0.869 Fit side-chains REVERT: A 98 GLU cc_start: 0.8430 (mp0) cc_final: 0.8136 (mp0) REVERT: B 98 GLU cc_start: 0.8408 (mp0) cc_final: 0.8122 (mp0) REVERT: B 105 ARG cc_start: 0.8468 (ttp80) cc_final: 0.7922 (mtm110) REVERT: C 98 GLU cc_start: 0.8413 (mp0) cc_final: 0.8100 (mp0) REVERT: D 98 GLU cc_start: 0.8413 (mp0) cc_final: 0.8101 (mp0) REVERT: D 399 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7609 (tp30) REVERT: E 105 ARG cc_start: 0.8479 (ttp80) cc_final: 0.7897 (ttp-170) REVERT: F 98 GLU cc_start: 0.8417 (mp0) cc_final: 0.8155 (mp0) REVERT: F 105 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7829 (ttm-80) REVERT: G 98 GLU cc_start: 0.8415 (mp0) cc_final: 0.8106 (mp0) REVERT: G 105 ARG cc_start: 0.8466 (ttp80) cc_final: 0.7869 (ttp-110) REVERT: H 105 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7893 (ttp-170) outliers start: 43 outliers final: 33 residues processed: 426 average time/residue: 0.7898 time to fit residues: 374.9528 Evaluate side-chains 406 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 373 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 163 optimal weight: 0.1980 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 303 optimal weight: 0.0070 chunk 124 optimal weight: 0.9980 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.123818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100300 restraints weight = 20178.994| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.19 r_work: 0.2986 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 24072 Z= 0.106 Angle : 0.483 4.343 32568 Z= 0.271 Chirality : 0.041 0.142 3712 Planarity : 0.003 0.031 4120 Dihedral : 9.169 99.740 3440 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.08 % Allowed : 8.01 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 1.11 (0.15), residues: 3024 helix: 1.74 (0.15), residues: 1240 sheet: -0.23 (0.24), residues: 384 loop : 0.22 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 480 TYR 0.009 0.001 TYR C 353 PHE 0.009 0.002 PHE D 401 HIS 0.002 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (24064) covalent geometry : angle 0.48252 / 0.27 (32568) hydrogen bonds : bond 0.04894 / 3.23 ( 1022) hydrogen bonds : angle 5.26273 / 3.62 ( 2859) Misc. bond : bond 0.00007 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 368 time to evaluate : 0.891 Fit side-chains REVERT: A 98 GLU cc_start: 0.8394 (mp0) cc_final: 0.8076 (mp0) REVERT: A 105 ARG cc_start: 0.8503 (ttp80) cc_final: 0.7815 (ttp-170) REVERT: B 98 GLU cc_start: 0.8361 (mp0) cc_final: 0.8097 (mp0) REVERT: B 105 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7903 (ttp-170) REVERT: C 105 ARG cc_start: 0.8501 (ttp80) cc_final: 0.7779 (ttm-80) REVERT: C 450 LYS cc_start: 0.8435 (mttp) cc_final: 0.8192 (mttp) REVERT: D 98 GLU cc_start: 0.8377 (mp0) cc_final: 0.8143 (mp0) REVERT: D 399 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7548 (tp30) REVERT: D 450 LYS cc_start: 0.8461 (mttp) cc_final: 0.8204 (mttp) REVERT: E 105 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7817 (ttp-170) REVERT: F 105 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7824 (ttm-80) REVERT: F 450 LYS cc_start: 0.8434 (mttp) cc_final: 0.8148 (mttp) REVERT: G 98 GLU cc_start: 0.8389 (mp0) cc_final: 0.8167 (mp0) REVERT: G 105 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7911 (ttp-110) REVERT: H 105 ARG cc_start: 0.8528 (ttp80) cc_final: 0.7831 (ttp-170) outliers start: 51 outliers final: 31 residues processed: 416 average time/residue: 0.7805 time to fit residues: 362.2356 Evaluate side-chains 393 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 362 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 168 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 274 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 303 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096434 restraints weight = 20097.786| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.18 r_work: 0.2927 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 24072 Z= 0.225 Angle : 0.656 5.417 32568 Z= 0.366 Chirality : 0.050 0.264 3712 Planarity : 0.005 0.030 4120 Dihedral : 9.758 116.997 3440 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.88 % Allowed : 9.19 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.60 (0.15), residues: 3024 helix: 1.19 (0.14), residues: 1240 sheet: -0.40 (0.24), residues: 384 loop : 0.04 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 341 TYR 0.017 0.002 TYR C 4 PHE 0.016 0.003 PHE F 24 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.23 (24064) covalent geometry : angle 0.65595 / 0.37 (32568) hydrogen bonds : bond 0.07156 / 4.73 ( 1022) hydrogen bonds : angle 5.75384 / 3.98 ( 2859) Misc. bond : bond 0.00018 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 0.829 Fit side-chains REVERT: B 98 GLU cc_start: 0.8406 (mp0) cc_final: 0.8105 (mp0) REVERT: B 105 ARG cc_start: 0.8485 (ttp80) cc_final: 0.7922 (ttp-170) REVERT: D 98 GLU cc_start: 0.8421 (mp0) cc_final: 0.8091 (mp0) REVERT: D 399 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7591 (tp30) REVERT: E 105 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7898 (ttp-170) REVERT: F 98 GLU cc_start: 0.8409 (mp0) cc_final: 0.8157 (mp0) REVERT: G 98 GLU cc_start: 0.8423 (mp0) cc_final: 0.8093 (mp0) REVERT: H 105 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7896 (ttp-170) outliers start: 46 outliers final: 32 residues processed: 413 average time/residue: 0.8135 time to fit residues: 374.4431 Evaluate side-chains 404 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 279 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 228 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 52 optimal weight: 0.0870 chunk 258 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100405 restraints weight = 20266.609| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.19 r_work: 0.2987 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 24072 Z= 0.104 Angle : 0.481 4.310 32568 Z= 0.270 Chirality : 0.041 0.142 3712 Planarity : 0.003 0.031 4120 Dihedral : 9.047 98.238 3440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.55 % Allowed : 9.27 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 1.13 (0.15), residues: 3024 helix: 1.75 (0.15), residues: 1240 sheet: -0.18 (0.24), residues: 384 loop : 0.23 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 407 TYR 0.009 0.001 TYR E 353 PHE 0.009 0.002 PHE H 401 HIS 0.002 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (24064) covalent geometry : angle 0.48051 / 0.27 (32568) hydrogen bonds : bond 0.04801 / 3.17 ( 1022) hydrogen bonds : angle 5.21628 / 3.59 ( 2859) Misc. bond : bond 0.00004 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 371 time to evaluate : 0.973 Fit side-chains REVERT: A 105 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7815 (ttp-170) REVERT: B 98 GLU cc_start: 0.8358 (mp0) cc_final: 0.8133 (mp0) REVERT: B 105 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7879 (ttp-170) REVERT: C 105 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7779 (ttm-80) REVERT: C 450 LYS cc_start: 0.8383 (mttp) cc_final: 0.8111 (mttp) REVERT: D 98 GLU cc_start: 0.8387 (mp0) cc_final: 0.8126 (mp0) REVERT: D 399 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7566 (tp30) REVERT: D 450 LYS cc_start: 0.8432 (mttp) cc_final: 0.8120 (mttp) REVERT: F 450 LYS cc_start: 0.8401 (mttp) cc_final: 0.8096 (mttp) REVERT: G 98 GLU cc_start: 0.8384 (mp0) cc_final: 0.8124 (mp0) REVERT: G 450 LYS cc_start: 0.8406 (mttp) cc_final: 0.8147 (mttp) REVERT: H 105 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7837 (ttp-170) outliers start: 38 outliers final: 31 residues processed: 405 average time/residue: 0.8533 time to fit residues: 384.5172 Evaluate side-chains 396 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 216 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 153 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 265 GLN B 498 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN E 441 GLN E 498 GLN F 265 GLN G 21 GLN G 265 GLN H 265 GLN H 441 GLN H 498 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096039 restraints weight = 20065.853| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.18 r_work: 0.2921 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 24072 Z= 0.261 Angle : 0.701 5.891 32568 Z= 0.391 Chirality : 0.052 0.306 3712 Planarity : 0.005 0.029 4120 Dihedral : 9.798 118.232 3440 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.72 % Allowed : 9.68 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.49 (0.15), residues: 3024 helix: 1.07 (0.14), residues: 1240 sheet: -0.44 (0.24), residues: 384 loop : -0.00 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 341 TYR 0.017 0.003 TYR F 4 PHE 0.017 0.003 PHE F 24 HIS 0.006 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 (24064) covalent geometry : angle 0.70111 / 0.39 (32568) hydrogen bonds : bond 0.07592 / 5.01 ( 1022) hydrogen bonds : angle 5.84799 / 4.04 ( 2859) Misc. bond : bond 0.00040 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 365 time to evaluate : 0.797 Fit side-chains REVERT: B 105 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7991 (ttp-110) REVERT: D 98 GLU cc_start: 0.8433 (mp0) cc_final: 0.8099 (mp0) REVERT: D 399 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7608 (tp30) REVERT: G 98 GLU cc_start: 0.8433 (mp0) cc_final: 0.8094 (mp0) outliers start: 42 outliers final: 32 residues processed: 403 average time/residue: 0.7735 time to fit residues: 346.8750 Evaluate side-chains 396 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 285 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.098752 restraints weight = 20157.177| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.19 r_work: 0.2963 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24072 Z= 0.131 Angle : 0.531 4.392 32568 Z= 0.299 Chirality : 0.043 0.149 3712 Planarity : 0.004 0.031 4120 Dihedral : 9.264 105.156 3440 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.63 % Allowed : 9.44 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.90 (0.15), residues: 3024 helix: 1.52 (0.15), residues: 1240 sheet: -0.26 (0.24), residues: 384 loop : 0.12 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 407 TYR 0.010 0.002 TYR D 348 PHE 0.011 0.002 PHE H 401 HIS 0.003 0.001 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (24064) covalent geometry : angle 0.53071 / 0.30 (32568) hydrogen bonds : bond 0.05508 / 3.64 ( 1022) hydrogen bonds : angle 5.42210 / 3.74 ( 2859) Misc. bond : bond 0.00002 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 360 time to evaluate : 0.954 Fit side-chains REVERT: A 105 ARG cc_start: 0.8485 (ttp80) cc_final: 0.7872 (ttp-170) REVERT: A 385 MET cc_start: 0.9273 (ttm) cc_final: 0.8920 (ttm) REVERT: B 98 GLU cc_start: 0.8375 (mp0) cc_final: 0.8109 (mp0) REVERT: B 385 MET cc_start: 0.9262 (ttm) cc_final: 0.8906 (ttm) REVERT: C 450 LYS cc_start: 0.8426 (mttp) cc_final: 0.8142 (mttp) REVERT: D 98 GLU cc_start: 0.8417 (mp0) cc_final: 0.8087 (mp0) REVERT: D 385 MET cc_start: 0.9272 (ttm) cc_final: 0.8915 (ttm) REVERT: D 399 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7574 (tp30) REVERT: D 450 LYS cc_start: 0.8447 (mttp) cc_final: 0.8154 (mttp) REVERT: F 450 LYS cc_start: 0.8424 (mttp) cc_final: 0.8136 (mttp) REVERT: G 98 GLU cc_start: 0.8419 (mp0) cc_final: 0.8088 (mp0) REVERT: G 450 LYS cc_start: 0.8427 (mttp) cc_final: 0.8172 (mttp) REVERT: H 105 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7889 (ttp-170) outliers start: 40 outliers final: 31 residues processed: 398 average time/residue: 0.8367 time to fit residues: 370.4080 Evaluate side-chains 395 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 364 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 22 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 294 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 265 GLN C 265 GLN C 448 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.096296 restraints weight = 20236.781| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.19 r_work: 0.2925 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24072 Z= 0.234 Angle : 0.676 5.628 32568 Z= 0.378 Chirality : 0.051 0.281 3712 Planarity : 0.005 0.029 4120 Dihedral : 9.719 117.094 3440 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.51 % Allowed : 9.93 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.48 (0.15), residues: 3024 helix: 1.07 (0.14), residues: 1240 sheet: -0.43 (0.24), residues: 384 loop : -0.01 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 341 TYR 0.019 0.003 TYR B 4 PHE 0.017 0.003 PHE D 401 HIS 0.005 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (24064) covalent geometry : angle 0.67595 / 0.38 (32568) hydrogen bonds : bond 0.07295 / 4.82 ( 1022) hydrogen bonds : angle 5.79122 / 4.00 ( 2859) Misc. bond : bond 0.00024 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 362 time to evaluate : 0.962 Fit side-chains REVERT: A 98 GLU cc_start: 0.8442 (mp0) cc_final: 0.8138 (mp0) REVERT: A 105 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7900 (ttp-170) REVERT: B 98 GLU cc_start: 0.8422 (mp0) cc_final: 0.8074 (mp0) REVERT: D 98 GLU cc_start: 0.8444 (mp0) cc_final: 0.8101 (mp0) REVERT: D 399 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7608 (tp30) outliers start: 37 outliers final: 32 residues processed: 397 average time/residue: 0.8261 time to fit residues: 366.0244 Evaluate side-chains 403 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 252 optimal weight: 7.9990 chunk 280 optimal weight: 0.9980 chunk 282 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 301 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 265 GLN D 21 GLN G 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097957 restraints weight = 20131.500| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.19 r_work: 0.2951 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24072 Z= 0.156 Angle : 0.570 4.555 32568 Z= 0.321 Chirality : 0.045 0.158 3712 Planarity : 0.004 0.031 4120 Dihedral : 9.444 110.399 3440 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.59 % Allowed : 9.68 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.75 (0.15), residues: 3024 helix: 1.37 (0.15), residues: 1240 sheet: -0.33 (0.24), residues: 384 loop : 0.06 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 407 TYR 0.012 0.002 TYR B 4 PHE 0.013 0.002 PHE A 401 HIS 0.004 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (24064) covalent geometry : angle 0.56987 / 0.32 (32568) hydrogen bonds : bond 0.05972 / 3.95 ( 1022) hydrogen bonds : angle 5.54053 / 3.82 ( 2859) Misc. bond : bond 0.00008 / 0.00 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 353 time to evaluate : 0.940 Fit side-chains REVERT: A 105 ARG cc_start: 0.8528 (ttp80) cc_final: 0.7892 (ttp-170) REVERT: B 105 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7918 (ttp-170) REVERT: C 450 LYS cc_start: 0.8408 (mttp) cc_final: 0.8143 (mttp) REVERT: D 98 GLU cc_start: 0.8422 (mp0) cc_final: 0.8082 (mp0) REVERT: D 105 ARG cc_start: 0.8489 (ttp80) cc_final: 0.7875 (ttp-110) REVERT: D 399 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7583 (tp30) REVERT: E 105 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7887 (ttp-170) REVERT: F 450 LYS cc_start: 0.8406 (mttp) cc_final: 0.8135 (mttp) REVERT: G 105 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7916 (ttp-170) REVERT: H 105 ARG cc_start: 0.8507 (ttp80) cc_final: 0.7890 (ttp-170) outliers start: 39 outliers final: 31 residues processed: 391 average time/residue: 0.8141 time to fit residues: 354.5624 Evaluate side-chains 392 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN B 265 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 21 GLN D 243 GLN D 265 GLN D 283 GLN D 441 GLN E 243 GLN E 265 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN G 283 GLN G 498 GLN H 265 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.095848 restraints weight = 19997.551| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.18 r_work: 0.2919 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 24072 Z= 0.274 Angle : 0.728 5.977 32568 Z= 0.407 Chirality : 0.054 0.330 3712 Planarity : 0.005 0.029 4120 Dihedral : 9.821 118.355 3440 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.43 % Allowed : 10.25 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % 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: 0.30 (0.14), residues: 3024 helix: 0.89 (0.14), residues: 1240 sheet: -0.54 (0.24), residues: 384 loop : -0.07 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 341 TYR 0.023 0.003 TYR B 4 PHE 0.018 0.004 PHE F 24 HIS 0.006 0.002 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 (24064) covalent geometry : angle 0.72794 / 0.41 (32568) hydrogen bonds : bond 0.07771 / 5.14 ( 1022) hydrogen bonds : angle 5.86988 / 4.05 ( 2859) Misc. bond : bond 0.00032 / 0.02 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10250.52 seconds wall clock time: 175 minutes 4.20 seconds (10504.20 seconds total)