Starting phenix.real_space_refine on Fri Aug 7 20:13:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_29357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_29357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_29357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_29357.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_29357.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_29357.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_29357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foz_29357/08_2026/8foz_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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23648 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "B" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "C" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "E" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "F" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "G" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "H" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 5.60, per 1000 atoms: 0.24 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.74 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: 5.18 Time building geometry restraints manager: 2.66 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 - 1.86: 31048 1.86 - 3.73: 1242 3.73 - 5.59: 180 5.59 - 7.45: 52 7.45 - 9.32: 46 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=" C1' IMP A 601 " pdb=" C2' IMP A 601 " pdb=" C3' IMP A 601 " ideal model delta sigma weight residual 111.00 101.68 9.32 3.00e+00 1.11e-01 9.65e+00 ... (remaining 32563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 13429 26.09 - 52.18: 701 52.18 - 78.27: 76 78.27 - 104.36: 30 104.36 - 130.45: 4 Dihedral angle restraints: 14240 sinusoidal: 5544 harmonic: 8696 Sorted by residual: dihedral pdb=" C5' IMP H 601 " pdb=" O5' IMP H 601 " pdb=" P IMP H 601 " pdb=" O2P IMP H 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.48 130.45 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" C5' IMP F 601 " pdb=" O5' IMP F 601 " pdb=" P IMP F 601 " pdb=" O2P IMP F 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.65 130.28 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.69 130.24 1 2.00e+01 2.50e-03 3.95e+01 ... (remaining 14237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2736 0.064 - 0.127: 875 0.127 - 0.191: 70 0.191 - 0.254: 15 0.254 - 0.318: 16 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: 5.210 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.280 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.139 24072 Z= 0.421 Angle : 0.956 9.318 32568 Z= 0.491 Chirality : 0.060 0.318 3712 Planarity : 0.005 0.040 4120 Dihedral : 15.665 130.450 8720 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.31 % Allowed : 8.91 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3024 helix: 0.71 (0.14), residues: 1232 sheet: -0.42 (0.24), residues: 384 loop : -0.05 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 412 TYR 0.039 0.004 TYR E 4 PHE 0.019 0.004 PHE G 24 HIS 0.005 0.002 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00893 / 0.42 (24064) covalent geometry : angle 0.95635 / 0.49 (32568) hydrogen bonds : bond 0.13963 / 9.27 ( 1022) hydrogen bonds : angle 6.39720 / 4.42 ( 2859) Misc. bond : bond 0.00046 / 0.02 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 369 time to evaluate : 0.853 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: 0.8381 time to fit residues: 371.6381 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 : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097506 restraints weight = 20092.105| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.19 r_work: 0.2944 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.0616 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= 0.169 Angle : 0.631 8.392 32568 Z= 0.340 Chirality : 0.046 0.200 3712 Planarity : 0.004 0.031 4120 Dihedral : 9.863 116.920 3444 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.43 % Allowed : 7.76 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3024 helix: 1.24 (0.15), residues: 1240 sheet: -0.44 (0.23), residues: 384 loop : 0.09 (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 F 24 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (24064) covalent geometry : angle 0.63109 / 0.34 (32568) hydrogen bonds : bond 0.06419 / 4.24 ( 1022) hydrogen bonds : angle 5.65896 / 3.90 ( 2859) Misc. bond : bond 0.00022 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 370 time to evaluate : 1.099 Fit side-chains REVERT: A 98 GLU cc_start: 0.8416 (mp0) cc_final: 0.8214 (mp0) REVERT: B 105 ARG cc_start: 0.8461 (ttp80) cc_final: 0.7972 (ttp-110) REVERT: D 98 GLU cc_start: 0.8385 (mp0) cc_final: 0.8092 (mp0) REVERT: D 399 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7569 (tp30) REVERT: E 105 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7978 (ttp-110) REVERT: G 98 GLU cc_start: 0.8398 (mp0) cc_final: 0.8112 (mp0) REVERT: G 105 ARG cc_start: 0.8471 (ttp80) cc_final: 0.7896 (ttp-170) REVERT: H 105 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7901 (ttp-170) outliers start: 35 outliers final: 31 residues processed: 400 average time/residue: 0.8603 time to fit residues: 383.2043 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 : 0.903 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN B 265 GLN B 498 GLN C 498 GLN D 21 GLN D 243 GLN D 498 GLN E 265 GLN E 498 GLN F 265 GLN F 498 GLN G 265 GLN G 498 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 = 0.3356 r_free = 0.3356 target = 0.119257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.095558 restraints weight = 20135.504| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.19 r_work: 0.2914 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.0556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 24072 Z= 0.273 Angle : 0.767 8.940 32568 Z= 0.414 Chirality : 0.054 0.330 3712 Planarity : 0.005 0.033 4120 Dihedral : 9.975 120.590 3440 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.76 % Allowed : 8.33 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3024 helix: 0.82 (0.14), residues: 1240 sheet: -0.57 (0.23), residues: 384 loop : -0.06 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 341 TYR 0.022 0.003 TYR G 4 PHE 0.017 0.004 PHE D 24 HIS 0.006 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (24064) covalent geometry : angle 0.76737 / 0.41 (32568) hydrogen bonds : bond 0.07906 / 5.22 ( 1022) hydrogen bonds : angle 5.93951 / 4.11 ( 2859) Misc. bond : bond 0.00021 / 0.01 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 375 time to evaluate : 0.899 Fit side-chains REVERT: A 98 GLU cc_start: 0.8441 (mp0) cc_final: 0.8134 (mp0) REVERT: B 98 GLU cc_start: 0.8425 (mp0) cc_final: 0.8111 (mp0) REVERT: B 105 ARG cc_start: 0.8449 (ttp80) cc_final: 0.7914 (mtm110) REVERT: C 98 GLU cc_start: 0.8436 (mp0) cc_final: 0.8151 (mp0) REVERT: D 98 GLU cc_start: 0.8426 (mp0) cc_final: 0.8098 (mp0) REVERT: D 399 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7605 (tp30) REVERT: E 105 ARG cc_start: 0.8459 (ttp80) cc_final: 0.7923 (mtm110) REVERT: F 98 GLU cc_start: 0.8443 (mp0) cc_final: 0.8154 (mp0) REVERT: G 98 GLU cc_start: 0.8427 (mp0) cc_final: 0.8104 (mp0) outliers start: 43 outliers final: 33 residues processed: 415 average time/residue: 0.7655 time to fit residues: 354.4167 Evaluate side-chains 415 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 382 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 6.9990 chunk 97 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.097290 restraints weight = 20122.974| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.19 r_work: 0.2941 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.0748 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= 0.169 Angle : 0.622 8.470 32568 Z= 0.335 Chirality : 0.046 0.189 3712 Planarity : 0.004 0.032 4120 Dihedral : 9.658 116.646 3440 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.47 % Allowed : 8.78 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3024 helix: 1.26 (0.15), residues: 1240 sheet: -0.46 (0.23), residues: 384 loop : 0.05 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 512 TYR 0.013 0.002 TYR E 4 PHE 0.014 0.002 PHE H 401 HIS 0.004 0.001 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (24064) covalent geometry : angle 0.62196 / 0.34 (32568) hydrogen bonds : bond 0.06309 / 4.17 ( 1022) hydrogen bonds : angle 5.62296 / 3.88 ( 2859) Misc. bond : bond 0.00004 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 381 time to evaluate : 0.970 Fit side-chains REVERT: A 98 GLU cc_start: 0.8412 (mp0) cc_final: 0.8091 (mp0) REVERT: A 105 ARG cc_start: 0.8466 (ttp80) cc_final: 0.7881 (ttp-170) REVERT: B 98 GLU cc_start: 0.8396 (mp0) cc_final: 0.8133 (mp0) REVERT: B 105 ARG cc_start: 0.8472 (ttp80) cc_final: 0.7926 (mtm110) REVERT: D 98 GLU cc_start: 0.8407 (mp0) cc_final: 0.8061 (mp0) REVERT: D 399 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7584 (tp30) REVERT: E 105 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7929 (mtm110) REVERT: G 98 GLU cc_start: 0.8420 (mp0) cc_final: 0.8077 (mp0) REVERT: H 105 ARG cc_start: 0.8494 (ttp80) cc_final: 0.7915 (ttp-170) outliers start: 36 outliers final: 33 residues processed: 412 average time/residue: 0.8332 time to fit residues: 383.0181 Evaluate side-chains 412 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 379 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 0.9990 chunk 120 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 189 optimal weight: 0.0770 chunk 274 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.121685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098071 restraints weight = 20116.529| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.19 r_work: 0.2952 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: 0.9135 moved from start: 0.0877 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= 0.144 Angle : 0.582 8.364 32568 Z= 0.312 Chirality : 0.044 0.152 3712 Planarity : 0.004 0.032 4120 Dihedral : 9.440 111.003 3440 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.25 % Allowed : 8.42 % 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 are not related in a simple way. whole: 0.87 (0.15), residues: 3024 helix: 1.50 (0.15), residues: 1240 sheet: -0.37 (0.23), residues: 384 loop : 0.13 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 512 TYR 0.011 0.002 TYR H 348 PHE 0.012 0.002 PHE H 401 HIS 0.003 0.001 HIS G 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (24064) covalent geometry : angle 0.58234 / 0.31 (32568) hydrogen bonds : bond 0.05812 / 3.84 ( 1022) hydrogen bonds : angle 5.47968 / 3.78 ( 2859) Misc. bond : bond 0.00004 / 0.00 ( 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 433 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 378 time to evaluate : 0.919 Fit side-chains REVERT: A 98 GLU cc_start: 0.8424 (mp0) cc_final: 0.8087 (mp0) REVERT: A 105 ARG cc_start: 0.8487 (ttp80) cc_final: 0.7882 (ttp-170) REVERT: B 105 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7940 (mtm110) REVERT: D 98 GLU cc_start: 0.8411 (mp0) cc_final: 0.8162 (mp0) REVERT: D 399 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7594 (tp30) REVERT: E 105 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7923 (ttp-170) REVERT: F 98 GLU cc_start: 0.8412 (mp0) cc_final: 0.8210 (mp0) REVERT: F 450 LYS cc_start: 0.8411 (mttp) cc_final: 0.8131 (mttp) REVERT: G 98 GLU cc_start: 0.8418 (mp0) cc_final: 0.8159 (mp0) REVERT: H 105 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7943 (ttp-170) outliers start: 55 outliers final: 36 residues processed: 424 average time/residue: 0.8509 time to fit residues: 401.6159 Evaluate side-chains 406 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 370 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 75 GLU 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 75 GLU 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 75 GLU 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: 0.9980 chunk 173 optimal weight: 0.0060 chunk 202 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 258 optimal weight: 0.6980 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 265 GLN C 265 GLN D 21 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097293 restraints weight = 20189.721| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.19 r_work: 0.2940 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.0820 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= 0.167 Angle : 0.623 8.616 32568 Z= 0.334 Chirality : 0.046 0.187 3712 Planarity : 0.004 0.033 4120 Dihedral : 9.551 116.612 3440 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.39 % Allowed : 9.68 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.15), residues: 3024 helix: 1.38 (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 0.003 0.000 ARG H 341 TYR 0.013 0.002 TYR A 348 PHE 0.014 0.002 PHE D 401 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (24064) covalent geometry : angle 0.62267 / 0.33 (32568) hydrogen bonds : bond 0.06289 / 4.16 ( 1022) hydrogen bonds : angle 5.56504 / 3.84 ( 2859) Misc. bond : bond 0.00002 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 0.917 Fit side-chains REVERT: A 105 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7901 (ttp-170) REVERT: A 385 MET cc_start: 0.9255 (ttm) cc_final: 0.8961 (ttm) REVERT: B 98 GLU cc_start: 0.8429 (mp0) cc_final: 0.8205 (mp0) REVERT: B 105 ARG cc_start: 0.8481 (ttp80) cc_final: 0.7910 (mtm110) REVERT: C 450 LYS cc_start: 0.8416 (mttp) cc_final: 0.8149 (mttp) REVERT: D 399 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7583 (tp30) REVERT: E 105 ARG cc_start: 0.8484 (ttp80) cc_final: 0.7887 (ttp-170) REVERT: F 385 MET cc_start: 0.9255 (ttm) cc_final: 0.8957 (ttm) REVERT: F 450 LYS cc_start: 0.8411 (mttp) cc_final: 0.8140 (mttp) REVERT: G 98 GLU cc_start: 0.8408 (mp0) cc_final: 0.8108 (mp0) REVERT: G 385 MET cc_start: 0.9260 (ttm) cc_final: 0.8961 (ttm) REVERT: H 105 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7894 (ttp-170) outliers start: 34 outliers final: 33 residues processed: 389 average time/residue: 0.8416 time to fit residues: 364.9822 Evaluate side-chains 404 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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: 7.9990 chunk 48 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 216 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 153 optimal weight: 0.0870 chunk 97 optimal weight: 0.0870 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100376 restraints weight = 20155.788| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.19 r_work: 0.2987 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24072 Z= 0.106 Angle : 0.519 7.964 32568 Z= 0.277 Chirality : 0.041 0.141 3712 Planarity : 0.003 0.032 4120 Dihedral : 9.040 99.043 3440 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.92 % Allowed : 9.15 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.15), residues: 3024 helix: 1.79 (0.15), residues: 1240 sheet: -0.16 (0.24), residues: 384 loop : 0.25 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 512 TYR 0.010 0.001 TYR E 353 PHE 0.009 0.002 PHE H 401 HIS 0.002 0.001 HIS F 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (24064) covalent geometry : angle 0.51909 / 0.28 (32568) hydrogen bonds : bond 0.04796 / 3.17 ( 1022) hydrogen bonds : angle 5.20175 / 3.58 ( 2859) Misc. bond : bond 0.00004 / 0.00 ( 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 400 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 353 time to evaluate : 0.933 Fit side-chains REVERT: A 98 GLU cc_start: 0.8412 (mp0) cc_final: 0.8105 (mp0) REVERT: A 105 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7817 (ttp-170) REVERT: B 105 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7872 (ttp-170) REVERT: C 450 LYS cc_start: 0.8389 (mttp) cc_final: 0.8094 (mttp) REVERT: D 399 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7577 (tp30) REVERT: D 450 LYS cc_start: 0.8437 (mttp) cc_final: 0.8127 (mttp) REVERT: E 105 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7860 (ttp-170) REVERT: F 450 LYS cc_start: 0.8395 (mttp) cc_final: 0.8088 (mttp) REVERT: G 98 GLU cc_start: 0.8394 (mp0) cc_final: 0.8138 (mp0) REVERT: G 450 LYS cc_start: 0.8414 (mttp) cc_final: 0.8144 (mttp) REVERT: H 105 ARG cc_start: 0.8512 (ttp80) cc_final: 0.7883 (ttp-170) outliers start: 47 outliers final: 32 residues processed: 398 average time/residue: 0.8450 time to fit residues: 374.9871 Evaluate side-chains 384 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 352 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 75 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 285 optimal weight: 0.5980 chunk 173 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 240 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 265 GLN C 265 GLN C 448 GLN D 21 GLN D 265 GLN E 265 GLN E 368 GLN F 265 GLN F 448 GLN G 21 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.097773 restraints weight = 20114.862| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.19 r_work: 0.2947 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24072 Z= 0.160 Angle : 0.608 8.577 32568 Z= 0.325 Chirality : 0.045 0.174 3712 Planarity : 0.004 0.031 4120 Dihedral : 9.424 114.475 3440 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.31 % Allowed : 9.76 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 3024 helix: 1.50 (0.15), residues: 1240 sheet: -0.23 (0.24), residues: 384 loop : 0.15 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 341 TYR 0.013 0.002 TYR A 348 PHE 0.013 0.002 PHE H 401 HIS 0.004 0.001 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (24064) covalent geometry : angle 0.60834 / 0.33 (32568) hydrogen bonds : bond 0.06095 / 4.03 ( 1022) hydrogen bonds : angle 5.51469 / 3.81 ( 2859) Misc. bond : bond 0.00004 / 0.00 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 351 time to evaluate : 0.928 Fit side-chains REVERT: A 98 GLU cc_start: 0.8435 (mp0) cc_final: 0.8148 (mp0) REVERT: A 105 ARG cc_start: 0.8470 (ttp80) cc_final: 0.7885 (ttp-170) REVERT: B 98 GLU cc_start: 0.8393 (mp0) cc_final: 0.8067 (mp0) REVERT: C 450 LYS cc_start: 0.8400 (mttp) cc_final: 0.8137 (mttp) REVERT: D 399 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7579 (tp30) REVERT: F 450 LYS cc_start: 0.8399 (mttp) cc_final: 0.8120 (mttp) REVERT: G 98 GLU cc_start: 0.8408 (mp0) cc_final: 0.8111 (mp0) REVERT: H 105 ARG cc_start: 0.8507 (ttp80) cc_final: 0.7912 (ttp-170) outliers start: 32 outliers final: 32 residues processed: 382 average time/residue: 0.8598 time to fit residues: 365.8285 Evaluate side-chains 377 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 75 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 22 optimal weight: 8.9990 chunk 233 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 441 GLN B 265 GLN B 441 GLN C 265 GLN D 21 GLN D 265 GLN D 441 GLN E 265 GLN E 441 GLN F 265 GLN G 265 GLN H 265 GLN H 441 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.096332 restraints weight = 20211.582| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.19 r_work: 0.2926 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24072 Z= 0.224 Angle : 0.699 8.808 32568 Z= 0.377 Chirality : 0.050 0.267 3712 Planarity : 0.004 0.029 4120 Dihedral : 9.678 119.382 3440 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.31 % Allowed : 10.01 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3024 helix: 1.13 (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 0.005 0.001 ARG C 341 TYR 0.018 0.002 TYR B 4 PHE 0.016 0.003 PHE F 24 HIS 0.005 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (24064) covalent geometry : angle 0.69943 / 0.38 (32568) hydrogen bonds : bond 0.07156 / 4.73 ( 1022) hydrogen bonds : angle 5.74274 / 3.97 ( 2859) Misc. bond : bond 0.00005 / 0.00 ( 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 384 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 352 time to evaluate : 0.898 Fit side-chains REVERT: A 105 ARG cc_start: 0.8509 (ttp80) cc_final: 0.7895 (ttp-170) REVERT: B 98 GLU cc_start: 0.8417 (mp0) cc_final: 0.8080 (mp0) REVERT: D 399 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7605 (tp30) REVERT: G 98 GLU cc_start: 0.8442 (mp0) cc_final: 0.8094 (mp0) outliers start: 32 outliers final: 31 residues processed: 383 average time/residue: 0.8333 time to fit residues: 356.6941 Evaluate side-chains 388 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 357 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 252 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 282 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 301 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.096921 restraints weight = 20100.840| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.19 r_work: 0.2934 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.0833 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= 0.196 Angle : 0.658 8.607 32568 Z= 0.355 Chirality : 0.048 0.221 3712 Planarity : 0.004 0.030 4120 Dihedral : 9.624 118.103 3440 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.63 % Allowed : 9.84 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.15), residues: 3024 helix: 1.19 (0.14), residues: 1240 sheet: -0.40 (0.24), residues: 384 loop : 0.04 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 341 TYR 0.016 0.002 TYR B 4 PHE 0.015 0.003 PHE G 514 HIS 0.004 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (24064) covalent geometry : angle 0.65805 / 0.36 (32568) hydrogen bonds : bond 0.06636 / 4.39 ( 1022) hydrogen bonds : angle 5.69409 / 3.93 ( 2859) Misc. bond : bond 0.00012 / 0.01 ( 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 398 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.845 Fit side-chains REVERT: A 98 GLU cc_start: 0.8432 (mp0) cc_final: 0.8089 (mp0) REVERT: A 105 ARG cc_start: 0.8515 (ttp80) cc_final: 0.7895 (ttp-170) REVERT: B 98 GLU cc_start: 0.8409 (mp0) cc_final: 0.8068 (mp0) REVERT: D 399 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7603 (tp30) REVERT: H 105 ARG cc_start: 0.8484 (ttp80) cc_final: 0.7896 (ttp-170) outliers start: 40 outliers final: 31 residues processed: 396 average time/residue: 0.7432 time to fit residues: 327.8167 Evaluate side-chains 387 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 356 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 226 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 272 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.098145 restraints weight = 20022.485| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.18 r_work: 0.2954 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.0957 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= 0.149 Angle : 0.595 8.340 32568 Z= 0.321 Chirality : 0.044 0.153 3712 Planarity : 0.004 0.031 4120 Dihedral : 9.414 112.047 3440 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.35 % Allowed : 10.13 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.15), residues: 3024 helix: 1.45 (0.15), residues: 1240 sheet: -0.30 (0.24), residues: 384 loop : 0.12 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 407 TYR 0.012 0.002 TYR E 4 PHE 0.014 0.002 PHE G 514 HIS 0.004 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (24064) covalent geometry : angle 0.59494 / 0.32 (32568) hydrogen bonds : bond 0.05807 / 3.84 ( 1022) hydrogen bonds : angle 5.50547 / 3.79 ( 2859) Misc. bond : bond 0.00003 / 0.00 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10742.94 seconds wall clock time: 183 minutes 28.63 seconds (11008.63 seconds total)