Starting phenix.real_space_refine on Sun Aug 24 23:47:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foz_29357/08_2025/8foz_29357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foz_29357/08_2025/8foz_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 { model { file = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2025/8foz_29357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2025/8foz_29357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2025/8foz_29357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2025/8foz_29357.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 5.44, per 1000 atoms: 0.23 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: 1.59 Conformation dependent library (CDL) restraints added in 974.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.80 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: 4.32 Time building geometry restraints manager: 2.29 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: 13768 26.09 - 52.18: 757 52.18 - 78.27: 80 78.27 - 104.36: 31 104.36 - 130.45: 4 Dihedral angle restraints: 14640 sinusoidal: 5944 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 14637 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: 6.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.430 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 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 : 15.789 130.450 9120 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 aren 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 covalent geometry : bond 0.00891 (24064) covalent geometry : angle 0.91870 (32568) hydrogen bonds : bond 0.13963 ( 1022) hydrogen bonds : angle 6.39720 ( 2859) Misc. bond : bond 0.00046 ( 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 : 0.865 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: 0.6906 time to fit residues: 305.6213 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 : 0.800 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 243 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.097601 restraints weight = 20095.303| |-----------------------------------------------------------------------------| 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: 0.2838 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.0626 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 4.770 32568 Z= 0.333 Chirality : 0.046 0.199 3712 Planarity : 0.004 0.030 4120 Dihedral : 10.642 114.487 3844 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.22 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 aren not related in a simple way. whole: 0.67 (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 covalent geometry : bond 0.00363 (24064) covalent geometry : angle 0.59181 (32568) hydrogen bonds : bond 0.06401 ( 1022) hydrogen bonds : angle 5.65387 ( 2859) Misc. bond : bond 0.00004 ( 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 404 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 369 time to evaluate : 0.817 Fit side-chains REVERT: A 98 GLU cc_start: 0.8418 (mp0) cc_final: 0.8216 (mp0) REVERT: B 105 ARG cc_start: 0.8462 (ttp80) cc_final: 0.7972 (ttp-110) REVERT: D 98 GLU cc_start: 0.8381 (mp0) cc_final: 0.8087 (mp0) REVERT: D 399 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7574 (tp30) REVERT: E 105 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8022 (ttp-110) REVERT: G 98 GLU cc_start: 0.8398 (mp0) cc_final: 0.8115 (mp0) REVERT: G 105 ARG cc_start: 0.8471 (ttp80) cc_final: 0.7894 (ttp-170) REVERT: H 105 ARG cc_start: 0.8484 (ttp80) cc_final: 0.7945 (ttp-170) outliers start: 35 outliers final: 31 residues processed: 399 average time/residue: 0.6784 time to fit residues: 300.7417 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 : 0.711 ------------------------------------------------------------------------------- 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: 3.9990 chunk 50 optimal weight: 6.9990 chunk 255 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 256 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 153 optimal weight: 0.0040 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN D 21 GLN E 265 GLN F 265 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098542 restraints weight = 20159.263| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.19 r_work: 0.2959 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.0822 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= 0.138 Angle : 0.537 4.395 32568 Z= 0.302 Chirality : 0.043 0.152 3712 Planarity : 0.004 0.031 4120 Dihedral : 10.188 107.263 3840 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.08 % Allowed : 7.92 % Favored : 89.99 % 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 aren not related in a simple way. whole: 0.90 (0.15), residues: 3024 helix: 1.53 (0.15), residues: 1240 sheet: -0.38 (0.24), residues: 384 loop : 0.16 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.012 0.002 TYR G 4 PHE 0.012 0.002 PHE H 401 HIS 0.003 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00291 (24064) covalent geometry : angle 0.53696 (32568) hydrogen bonds : bond 0.05753 ( 1022) hydrogen bonds : angle 5.47647 ( 2859) Misc. bond : bond 0.00003 ( 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 424 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 373 time to evaluate : 0.575 Fit side-chains REVERT: A 98 GLU cc_start: 0.8414 (mp0) cc_final: 0.8103 (mp0) REVERT: A 105 ARG cc_start: 0.8530 (ttp80) cc_final: 0.7863 (ttp-170) REVERT: B 98 GLU cc_start: 0.8401 (mp0) cc_final: 0.8148 (mp0) REVERT: D 98 GLU cc_start: 0.8390 (mp0) cc_final: 0.8132 (mp0) REVERT: D 399 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7566 (tp30) REVERT: F 450 LYS cc_start: 0.8476 (mttp) cc_final: 0.8191 (mttp) REVERT: G 98 GLU cc_start: 0.8402 (mp0) cc_final: 0.8145 (mp0) REVERT: G 105 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7963 (ttp-170) outliers start: 51 outliers final: 33 residues processed: 418 average time/residue: 0.7033 time to fit residues: 327.3700 Evaluate side-chains 388 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 355 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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: 8.9990 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN C 265 GLN D 21 GLN E 265 GLN F 265 GLN G 265 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.096672 restraints weight = 20086.603| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.19 r_work: 0.2931 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24072 Z= 0.201 Angle : 0.631 5.142 32568 Z= 0.353 Chirality : 0.048 0.238 3712 Planarity : 0.005 0.031 4120 Dihedral : 10.479 116.275 3840 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.80 % Allowed : 8.99 % Favored : 89.22 % 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 aren not related in a simple way. whole: 0.63 (0.15), residues: 3024 helix: 1.23 (0.14), residues: 1240 sheet: -0.43 (0.24), residues: 384 loop : 0.05 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 341 TYR 0.016 0.002 TYR C 4 PHE 0.015 0.003 PHE B 24 HIS 0.005 0.001 HIS H 466 Details of bonding type rmsd covalent geometry : bond 0.00442 (24064) covalent geometry : angle 0.63058 (32568) hydrogen bonds : bond 0.06901 ( 1022) hydrogen bonds : angle 5.70754 ( 2859) Misc. bond : bond 0.00016 ( 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 418 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 374 time to evaluate : 1.039 Fit side-chains REVERT: A 105 ARG cc_start: 0.8518 (ttp80) cc_final: 0.7890 (ttp-170) REVERT: B 98 GLU cc_start: 0.8414 (mp0) cc_final: 0.8094 (mp0) REVERT: B 105 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7900 (ttp-170) REVERT: C 98 GLU cc_start: 0.8416 (mp0) cc_final: 0.8185 (mp0) REVERT: C 105 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7846 (ttm-80) REVERT: D 98 GLU cc_start: 0.8412 (mp0) cc_final: 0.8077 (mp0) REVERT: D 399 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7585 (tp30) REVERT: E 105 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7897 (ttp-170) REVERT: F 98 GLU cc_start: 0.8421 (mp0) cc_final: 0.8187 (mp0) REVERT: G 98 GLU cc_start: 0.8415 (mp0) cc_final: 0.8082 (mp0) REVERT: G 105 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7901 (ttp-170) REVERT: H 105 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7908 (ttp-170) outliers start: 44 outliers final: 33 residues processed: 416 average time/residue: 0.9179 time to fit residues: 423.4555 Evaluate side-chains 416 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 383 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 168 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 191 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 274 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096646 restraints weight = 20054.630| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.18 r_work: 0.2930 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 24072 Z= 0.210 Angle : 0.636 5.174 32568 Z= 0.357 Chirality : 0.048 0.240 3712 Planarity : 0.005 0.030 4120 Dihedral : 10.491 115.787 3840 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.84 % Allowed : 8.82 % Favored : 89.34 % 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 aren not related in a simple way. whole: 0.54 (0.15), residues: 3024 helix: 1.13 (0.14), residues: 1240 sheet: -0.45 (0.24), residues: 384 loop : 0.03 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 341 TYR 0.017 0.002 TYR C 4 PHE 0.016 0.003 PHE G 401 HIS 0.005 0.001 HIS H 466 Details of bonding type rmsd covalent geometry : bond 0.00465 (24064) covalent geometry : angle 0.63591 (32568) hydrogen bonds : bond 0.06942 ( 1022) hydrogen bonds : angle 5.72745 ( 2859) Misc. bond : bond 0.00012 ( 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 439 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 394 time to evaluate : 0.986 Fit side-chains REVERT: A 105 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7892 (ttp-170) REVERT: B 98 GLU cc_start: 0.8411 (mp0) cc_final: 0.8046 (mp0) REVERT: B 105 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7894 (ttp-170) REVERT: C 105 ARG cc_start: 0.8472 (ttp80) cc_final: 0.7841 (ttm-80) REVERT: D 98 GLU cc_start: 0.8417 (mp0) cc_final: 0.8079 (mp0) REVERT: D 399 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7584 (tp30) REVERT: E 105 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7902 (ttp-170) REVERT: G 98 GLU cc_start: 0.8417 (mp0) cc_final: 0.8080 (mp0) REVERT: G 105 ARG cc_start: 0.8469 (ttp80) cc_final: 0.7897 (ttp-170) REVERT: H 105 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7895 (ttp-170) outliers start: 45 outliers final: 33 residues processed: 431 average time/residue: 0.9390 time to fit residues: 448.2856 Evaluate side-chains 401 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 368 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 279 optimal weight: 2.9990 chunk 173 optimal weight: 0.0570 chunk 202 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 overall best weight: 1.6704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097281 restraints weight = 20164.240| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.19 r_work: 0.2940 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.0784 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= 0.175 Angle : 0.590 4.667 32568 Z= 0.331 Chirality : 0.046 0.184 3712 Planarity : 0.004 0.033 4120 Dihedral : 10.376 113.937 3840 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.39 % Allowed : 9.07 % Favored : 89.54 % 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 aren not related in a simple way. whole: 0.67 (0.15), residues: 3024 helix: 1.27 (0.15), residues: 1240 sheet: -0.37 (0.24), residues: 384 loop : 0.07 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 341 TYR 0.014 0.002 TYR C 4 PHE 0.014 0.002 PHE H 401 HIS 0.004 0.001 HIS G 466 Details of bonding type rmsd covalent geometry : bond 0.00381 (24064) covalent geometry : angle 0.58983 (32568) hydrogen bonds : bond 0.06370 ( 1022) hydrogen bonds : angle 5.63065 ( 2859) Misc. bond : bond 0.00011 ( 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 410 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 376 time to evaluate : 0.970 Fit side-chains REVERT: A 98 GLU cc_start: 0.8447 (mp0) cc_final: 0.8235 (mp0) REVERT: A 105 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7887 (ttp-170) REVERT: B 98 GLU cc_start: 0.8401 (mp0) cc_final: 0.8053 (mp0) REVERT: B 105 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7892 (ttp-170) REVERT: C 98 GLU cc_start: 0.8428 (mp0) cc_final: 0.8137 (mp0) REVERT: D 399 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7589 (tp30) REVERT: E 105 ARG cc_start: 0.8490 (ttp80) cc_final: 0.7898 (ttp-170) REVERT: F 98 GLU cc_start: 0.8428 (mp0) cc_final: 0.8152 (mp0) REVERT: F 450 LYS cc_start: 0.8430 (mttp) cc_final: 0.8164 (mttp) REVERT: G 105 ARG cc_start: 0.8486 (ttp80) cc_final: 0.7905 (ttp-170) REVERT: H 105 ARG cc_start: 0.8501 (ttp80) cc_final: 0.7899 (ttp-170) outliers start: 34 outliers final: 33 residues processed: 405 average time/residue: 0.9083 time to fit residues: 408.2461 Evaluate side-chains 401 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 368 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 97 optimal weight: 0.0870 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 498 GLN B 498 GLN C 498 GLN D 21 GLN D 265 GLN D 498 GLN E 441 GLN E 498 GLN F 498 GLN G 265 GLN G 498 GLN H 441 GLN H 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.096037 restraints weight = 20043.662| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.18 r_work: 0.2921 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 24072 Z= 0.245 Angle : 0.685 5.703 32568 Z= 0.384 Chirality : 0.051 0.295 3712 Planarity : 0.005 0.031 4120 Dihedral : 10.555 117.437 3840 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.67 % Allowed : 9.31 % Favored : 89.01 % 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 aren not related in a simple way. whole: 0.36 (0.15), residues: 3024 helix: 0.93 (0.14), residues: 1240 sheet: -0.54 (0.23), residues: 384 loop : -0.01 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 341 TYR 0.019 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 covalent geometry : bond 0.00548 (24064) covalent geometry : angle 0.68540 (32568) hydrogen bonds : bond 0.07489 ( 1022) hydrogen bonds : angle 5.81894 ( 2859) Misc. bond : bond 0.00012 ( 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 416 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 0.972 Fit side-chains REVERT: A 98 GLU cc_start: 0.8475 (mp0) cc_final: 0.8159 (mp0) REVERT: C 98 GLU cc_start: 0.8446 (mp0) cc_final: 0.8155 (mp0) REVERT: D 399 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7608 (tp30) REVERT: F 98 GLU cc_start: 0.8451 (mp0) cc_final: 0.8157 (mp0) REVERT: H 105 ARG cc_start: 0.8463 (ttp80) cc_final: 0.7899 (ttp-170) outliers start: 41 outliers final: 33 residues processed: 410 average time/residue: 0.9215 time to fit residues: 418.8723 Evaluate side-chains 395 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 362 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 285 optimal weight: 5.9990 chunk 173 optimal weight: 0.0980 chunk 202 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 GLN D 265 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 = 0.121523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098110 restraints weight = 20152.380| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.18 r_work: 0.2954 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24072 Z= 0.145 Angle : 0.549 4.442 32568 Z= 0.310 Chirality : 0.044 0.154 3712 Planarity : 0.004 0.032 4120 Dihedral : 10.177 107.845 3840 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.35 % Allowed : 9.19 % Favored : 89.46 % 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 aren not related in a simple way. whole: 0.79 (0.15), residues: 3024 helix: 1.42 (0.15), residues: 1240 sheet: -0.37 (0.24), residues: 384 loop : 0.09 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 407 TYR 0.011 0.002 TYR E 348 PHE 0.012 0.002 PHE D 401 HIS 0.003 0.001 HIS E 466 Details of bonding type rmsd covalent geometry : bond 0.00307 (24064) covalent geometry : angle 0.54920 (32568) hydrogen bonds : bond 0.05807 ( 1022) hydrogen bonds : angle 5.49979 ( 2859) Misc. bond : bond 0.00008 ( 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 398 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.604 Fit side-chains REVERT: A 98 GLU cc_start: 0.8440 (mp0) cc_final: 0.8101 (mp0) REVERT: A 105 ARG cc_start: 0.8479 (ttp80) cc_final: 0.7884 (ttp-170) REVERT: B 98 GLU cc_start: 0.8398 (mp0) cc_final: 0.8163 (mp0) REVERT: B 105 ARG cc_start: 0.8492 (ttp80) cc_final: 0.7898 (ttp-170) REVERT: C 98 GLU cc_start: 0.8390 (mp0) cc_final: 0.8047 (mp0) REVERT: C 450 LYS cc_start: 0.8402 (mttp) cc_final: 0.8145 (mttp) REVERT: D 399 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7582 (tp30) REVERT: E 105 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7883 (ttp-170) REVERT: F 450 LYS cc_start: 0.8409 (mttp) cc_final: 0.8139 (mttp) REVERT: G 105 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7918 (ttp-170) REVERT: H 105 ARG cc_start: 0.8508 (ttp80) cc_final: 0.7889 (ttp-170) outliers start: 33 outliers final: 33 residues processed: 393 average time/residue: 0.8606 time to fit residues: 375.1548 Evaluate side-chains 401 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 368 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 22 optimal weight: 8.9990 chunk 233 optimal weight: 1.9990 chunk 294 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 286 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 227 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3385 r_free = 0.3385 target = 0.121644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098109 restraints weight = 20238.907| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.19 r_work: 0.2953 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.0914 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= 0.148 Angle : 0.558 4.447 32568 Z= 0.314 Chirality : 0.044 0.155 3712 Planarity : 0.004 0.032 4120 Dihedral : 10.165 108.280 3840 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.67 % Allowed : 9.52 % Favored : 88.81 % 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 aren not related in a simple way. whole: 0.82 (0.15), residues: 3024 helix: 1.44 (0.15), residues: 1240 sheet: -0.29 (0.24), residues: 384 loop : 0.10 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 407 TYR 0.012 0.002 TYR A 348 PHE 0.012 0.002 PHE A 401 HIS 0.003 0.001 HIS H 466 Details of bonding type rmsd covalent geometry : bond 0.00315 (24064) covalent geometry : angle 0.55768 (32568) hydrogen bonds : bond 0.05889 ( 1022) hydrogen bonds : angle 5.50645 ( 2859) Misc. bond : bond 0.00010 ( 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 409 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 368 time to evaluate : 0.933 Fit side-chains REVERT: A 98 GLU cc_start: 0.8432 (mp0) cc_final: 0.8104 (mp0) REVERT: A 105 ARG cc_start: 0.8470 (ttp80) cc_final: 0.7887 (ttp-170) REVERT: B 98 GLU cc_start: 0.8410 (mp0) cc_final: 0.8150 (mp0) REVERT: B 105 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7901 (ttp-170) REVERT: C 98 GLU cc_start: 0.8389 (mp0) cc_final: 0.8109 (mp0) REVERT: C 450 LYS cc_start: 0.8399 (mttp) cc_final: 0.8137 (mttp) REVERT: D 399 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7575 (tp30) REVERT: E 105 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7907 (ttp-170) REVERT: F 98 GLU cc_start: 0.8389 (mp0) cc_final: 0.8103 (mp0) REVERT: F 450 LYS cc_start: 0.8404 (mttp) cc_final: 0.8133 (mttp) REVERT: G 105 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7918 (ttp-170) REVERT: H 105 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7894 (ttp-170) outliers start: 41 outliers final: 33 residues processed: 404 average time/residue: 0.8095 time to fit residues: 362.9350 Evaluate side-chains 396 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 363 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 252 optimal weight: 0.0570 chunk 280 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 220 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3383 r_free = 0.3383 target = 0.121477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097980 restraints weight = 20159.230| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.18 r_work: 0.2950 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: 0.8990 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24072 Z= 0.155 Angle : 0.569 4.465 32568 Z= 0.320 Chirality : 0.045 0.167 3712 Planarity : 0.004 0.031 4120 Dihedral : 10.163 109.286 3840 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.67 % Allowed : 9.52 % Favored : 88.81 % 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 aren not related in a simple way. whole: 0.80 (0.15), residues: 3024 helix: 1.40 (0.15), residues: 1240 sheet: -0.30 (0.24), residues: 384 loop : 0.10 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 407 TYR 0.012 0.002 TYR D 4 PHE 0.013 0.002 PHE H 401 HIS 0.004 0.001 HIS E 466 Details of bonding type rmsd covalent geometry : bond 0.00333 (24064) covalent geometry : angle 0.56915 (32568) hydrogen bonds : bond 0.06024 ( 1022) hydrogen bonds : angle 5.52141 ( 2859) Misc. bond : bond 0.00010 ( 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 407 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 366 time to evaluate : 0.654 Fit side-chains REVERT: A 98 GLU cc_start: 0.8431 (mp0) cc_final: 0.8087 (mp0) REVERT: A 105 ARG cc_start: 0.8517 (ttp80) cc_final: 0.7890 (ttp-170) REVERT: B 98 GLU cc_start: 0.8402 (mp0) cc_final: 0.8135 (mp0) REVERT: C 98 GLU cc_start: 0.8390 (mp0) cc_final: 0.8111 (mp0) REVERT: C 450 LYS cc_start: 0.8399 (mttp) cc_final: 0.8136 (mttp) REVERT: D 399 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7573 (tp30) REVERT: E 105 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7909 (ttp-170) REVERT: F 98 GLU cc_start: 0.8392 (mp0) cc_final: 0.8117 (mp0) REVERT: F 450 LYS cc_start: 0.8404 (mttp) cc_final: 0.8132 (mttp) REVERT: G 105 ARG cc_start: 0.8499 (ttp80) cc_final: 0.7921 (ttp-170) REVERT: H 105 ARG cc_start: 0.8510 (ttp80) cc_final: 0.7912 (ttp-170) outliers start: 41 outliers final: 33 residues processed: 403 average time/residue: 0.8091 time to fit residues: 362.4113 Evaluate side-chains 400 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 367 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3371 r_free = 0.3371 target = 0.120540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.096966 restraints weight = 20003.796| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.18 r_work: 0.2936 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.0804 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= 0.193 Angle : 0.627 5.028 32568 Z= 0.352 Chirality : 0.048 0.228 3712 Planarity : 0.004 0.031 4120 Dihedral : 10.345 114.994 3840 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.43 % Allowed : 9.93 % Favored : 88.64 % 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 aren not related in a simple way. whole: 0.60 (0.15), residues: 3024 helix: 1.20 (0.15), residues: 1240 sheet: -0.40 (0.24), residues: 384 loop : 0.03 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 341 TYR 0.017 0.002 TYR D 4 PHE 0.015 0.003 PHE C 24 HIS 0.004 0.001 HIS D 466 Details of bonding type rmsd covalent geometry : bond 0.00425 (24064) covalent geometry : angle 0.62740 (32568) hydrogen bonds : bond 0.06726 ( 1022) hydrogen bonds : angle 5.65688 ( 2859) Misc. bond : bond 0.00010 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10640.76 seconds wall clock time: 181 minutes 40.07 seconds (10900.07 seconds total)