Starting phenix.real_space_refine on Fri Jun 20 14:21:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foz_29357/06_2025/8foz_29357.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foz_29357/06_2025/8foz_29357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8foz_29357/06_2025/8foz_29357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foz_29357/06_2025/8foz_29357.map" model { file = "/net/cci-nas-00/data/ceres_data/8foz_29357/06_2025/8foz_29357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foz_29357/06_2025/8foz_29357.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23648 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "B" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "C" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "D" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "E" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "F" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "G" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "H" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2889 Classifications: {'peptide': 384} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 370} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 14.11, per 1000 atoms: 0.60 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: 5.39 Conformation dependent library (CDL) restraints added in 2.7 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: 2.83 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: 7.92 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3952 1.30 - 1.43: 5962 1.43 - 1.56: 13870 1.56 - 1.69: 40 1.69 - 1.82: 240 Bond restraints: 24064 Sorted by residual: bond pdb=" C5 IMP A 601 " pdb=" C6 IMP A 601 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C5 IMP E 601 " pdb=" C6 IMP E 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP H 601 " pdb=" C6 IMP H 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP G 601 " pdb=" C6 IMP G 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C5 IMP D 601 " pdb=" C6 IMP D 601 " ideal model delta sigma weight residual 1.390 1.528 -0.138 2.00e-02 2.50e+03 4.74e+01 ... (remaining 24059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 31072 1.84 - 3.67: 1247 3.67 - 5.51: 182 5.51 - 7.34: 37 7.34 - 9.18: 30 Bond angle restraints: 32568 Sorted by residual: angle pdb=" N GLY G 9 " pdb=" CA GLY G 9 " pdb=" C GLY G 9 " ideal model delta sigma weight residual 110.77 104.64 6.13 1.93e+00 2.68e-01 1.01e+01 angle pdb=" N GLY D 9 " pdb=" CA GLY D 9 " pdb=" C GLY D 9 " ideal model delta sigma weight residual 110.77 104.68 6.09 1.93e+00 2.68e-01 9.97e+00 angle pdb=" N GLY H 9 " pdb=" CA GLY H 9 " pdb=" C GLY H 9 " ideal model delta sigma weight residual 110.77 104.70 6.07 1.93e+00 2.68e-01 9.90e+00 angle pdb=" N GLY A 9 " pdb=" CA GLY A 9 " pdb=" C GLY A 9 " ideal model delta sigma weight residual 110.77 104.76 6.01 1.93e+00 2.68e-01 9.69e+00 angle pdb=" N GLY C 9 " pdb=" CA GLY C 9 " pdb=" C GLY C 9 " ideal model delta sigma weight residual 110.77 104.78 5.99 1.93e+00 2.68e-01 9.64e+00 ... (remaining 32563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.09: 13768 26.09 - 52.18: 757 52.18 - 78.27: 80 78.27 - 104.36: 31 104.36 - 130.45: 4 Dihedral angle restraints: 14640 sinusoidal: 5944 harmonic: 8696 Sorted by residual: dihedral pdb=" C5' IMP H 601 " pdb=" O5' IMP H 601 " pdb=" P IMP H 601 " pdb=" O2P IMP H 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.48 130.45 1 2.00e+01 2.50e-03 3.96e+01 dihedral pdb=" C5' IMP F 601 " pdb=" O5' IMP F 601 " pdb=" P IMP F 601 " pdb=" O2P IMP F 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.65 130.28 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" C5' IMP G 601 " pdb=" O5' IMP G 601 " pdb=" P IMP G 601 " pdb=" O2P IMP G 601 " ideal model delta sinusoidal sigma weight residual 191.93 61.69 130.24 1 2.00e+01 2.50e-03 3.95e+01 ... (remaining 14637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2735 0.064 - 0.127: 884 0.127 - 0.191: 70 0.191 - 0.254: 15 0.254 - 0.318: 8 Chirality restraints: 3712 Sorted by residual: chirality pdb=" CB VAL E 361 " pdb=" CA VAL E 361 " pdb=" CG1 VAL E 361 " pdb=" CG2 VAL E 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL H 361 " pdb=" CA VAL H 361 " pdb=" CG1 VAL H 361 " pdb=" CG2 VAL H 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB VAL A 361 " pdb=" CA VAL A 361 " pdb=" CG1 VAL A 361 " pdb=" CG2 VAL A 361 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3709 not shown) Planarity restraints: 4120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 4 " 0.021 2.00e-02 2.50e+03 1.61e-02 5.19e+00 pdb=" CG TYR E 4 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR E 4 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR E 4 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR E 4 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 4 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 4 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 4 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 4 " -0.021 2.00e-02 2.50e+03 1.60e-02 5.14e+00 pdb=" CG TYR D 4 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 4 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 4 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 4 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 4 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 4 " -0.021 2.00e-02 2.50e+03 1.60e-02 5.11e+00 pdb=" CG TYR A 4 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 4 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 4 " -0.000 2.00e-02 2.50e+03 ... (remaining 4117 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4508 2.77 - 3.30: 22596 3.30 - 3.84: 41452 3.84 - 4.37: 50664 4.37 - 4.90: 83912 Nonbonded interactions: 203132 Sorted by model distance: nonbonded pdb=" OD1 ASP A 418 " pdb=" NH1 ARG D 512 " model vdw 2.238 3.120 nonbonded pdb=" NH1 ARG G 512 " pdb=" OD1 ASP H 418 " model vdw 2.240 3.120 nonbonded pdb=" NH1 ARG A 512 " pdb=" OD1 ASP B 418 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP E 418 " pdb=" NH1 ARG H 512 " model vdw 2.260 3.120 nonbonded pdb=" NH1 ARG E 512 " pdb=" OD1 ASP F 418 " model vdw 2.268 3.120 ... (remaining 203127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 5.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 51.080 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.139 24072 Z= 0.420 Angle : 0.919 9.180 32568 Z= 0.483 Chirality : 0.059 0.318 3712 Planarity : 0.005 0.040 4120 Dihedral : 15.789 130.450 9120 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.31 % Allowed : 8.91 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (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 HIS 0.005 0.002 HIS E 466 PHE 0.019 0.004 PHE G 24 TYR 0.039 0.004 TYR E 4 ARG 0.005 0.001 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.13963 ( 1022) hydrogen bonds : angle 6.39720 ( 2859) covalent geometry : bond 0.00891 (24064) covalent geometry : angle 0.91870 (32568) Misc. bond : bond 0.00046 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 369 time to evaluate : 2.411 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: 1.7035 time to fit residues: 754.3172 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 : 2.465 ------------------------------------------------------------------------------- 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 256 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.097319 restraints weight = 20026.970| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.19 r_work: 0.2938 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.0590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24072 Z= 0.181 Angle : 0.611 4.880 32568 Z= 0.343 Chirality : 0.047 0.215 3712 Planarity : 0.004 0.030 4120 Dihedral : 10.692 115.088 3844 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.47 % Allowed : 7.92 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3024 helix: 1.18 (0.14), residues: 1240 sheet: -0.46 (0.23), residues: 384 loop : 0.08 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.014 0.003 PHE D 24 TYR 0.018 0.002 TYR G 4 ARG 0.003 0.001 ARG E 512 Details of bonding type rmsd hydrogen bonds : bond 0.06604 ( 1022) hydrogen bonds : angle 5.69790 ( 2859) covalent geometry : bond 0.00393 (24064) covalent geometry : angle 0.61085 (32568) Misc. bond : bond 0.00006 ( 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 411 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 375 time to evaluate : 2.574 Fit side-chains REVERT: A 98 GLU cc_start: 0.8430 (mp0) cc_final: 0.8204 (mp0) REVERT: B 105 ARG cc_start: 0.8456 (ttp80) cc_final: 0.7973 (ttp-110) REVERT: D 98 GLU cc_start: 0.8388 (mp0) cc_final: 0.8094 (mp0) REVERT: D 399 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7579 (tp30) REVERT: E 105 ARG cc_start: 0.8474 (ttp80) cc_final: 0.7980 (ttp-110) REVERT: G 98 GLU cc_start: 0.8401 (mp0) cc_final: 0.8115 (mp0) REVERT: G 105 ARG cc_start: 0.8465 (ttp80) cc_final: 0.7891 (ttp-170) REVERT: H 105 ARG cc_start: 0.8479 (ttp80) cc_final: 0.7902 (ttp-170) outliers start: 36 outliers final: 31 residues processed: 405 average time/residue: 1.7225 time to fit residues: 776.8010 Evaluate side-chains 392 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.6980 chunk 114 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 279 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 GLN E 265 GLN G 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.097066 restraints weight = 20035.982| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.18 r_work: 0.2937 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.0676 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= 0.181 Angle : 0.605 4.801 32568 Z= 0.340 Chirality : 0.046 0.186 3712 Planarity : 0.004 0.032 4120 Dihedral : 10.510 114.881 3840 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.72 % Allowed : 8.58 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3024 helix: 1.22 (0.14), residues: 1240 sheet: -0.47 (0.23), residues: 384 loop : 0.06 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 466 PHE 0.014 0.003 PHE H 401 TYR 0.015 0.002 TYR G 4 ARG 0.003 0.001 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.06594 ( 1022) hydrogen bonds : angle 5.67537 ( 2859) covalent geometry : bond 0.00393 (24064) covalent geometry : angle 0.60525 (32568) Misc. bond : bond 0.00006 ( 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 419 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 2.575 Fit side-chains REVERT: A 98 GLU cc_start: 0.8426 (mp0) cc_final: 0.8137 (mp0) REVERT: A 105 ARG cc_start: 0.8527 (ttp80) cc_final: 0.7883 (ttp-170) REVERT: B 105 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7923 (mtm110) REVERT: C 98 GLU cc_start: 0.8427 (mp0) cc_final: 0.8176 (mp0) REVERT: C 105 ARG cc_start: 0.8483 (ttp80) cc_final: 0.7848 (ttm-80) REVERT: D 98 GLU cc_start: 0.8408 (mp0) cc_final: 0.8110 (mp0) REVERT: D 399 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7562 (tp30) REVERT: E 105 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7907 (ttp-170) REVERT: F 98 GLU cc_start: 0.8429 (mp0) cc_final: 0.8171 (mp0) REVERT: F 105 ARG cc_start: 0.8470 (ttp80) cc_final: 0.7835 (ttm-80) REVERT: G 98 GLU cc_start: 0.8418 (mp0) cc_final: 0.8116 (mp0) REVERT: G 105 ARG cc_start: 0.8473 (ttp80) cc_final: 0.7870 (ttp-110) REVERT: H 105 ARG cc_start: 0.8487 (ttp80) cc_final: 0.7836 (ttp-170) REVERT: H 109 LYS cc_start: 0.8354 (mmpt) cc_final: 0.8137 (mmmt) outliers start: 42 outliers final: 32 residues processed: 417 average time/residue: 1.7969 time to fit residues: 835.1665 Evaluate side-chains 411 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 379 time to evaluate : 2.788 ------------------------------------------------------------------------------- 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 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 219 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 285 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 21 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.097150 restraints weight = 20186.604| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.19 r_work: 0.2939 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.0722 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= 0.177 Angle : 0.594 4.702 32568 Z= 0.334 Chirality : 0.046 0.196 3712 Planarity : 0.004 0.030 4120 Dihedral : 10.433 114.587 3840 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.92 % Allowed : 8.50 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.15), residues: 3024 helix: 1.28 (0.14), residues: 1240 sheet: -0.41 (0.24), residues: 384 loop : 0.05 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 466 PHE 0.015 0.002 PHE G 401 TYR 0.014 0.002 TYR F 4 ARG 0.003 0.000 ARG H 341 Details of bonding type rmsd hydrogen bonds : bond 0.06452 ( 1022) hydrogen bonds : angle 5.64193 ( 2859) covalent geometry : bond 0.00385 (24064) covalent geometry : angle 0.59388 (32568) Misc. bond : bond 0.00007 ( 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 428 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 381 time to evaluate : 2.949 Fit side-chains REVERT: A 98 GLU cc_start: 0.8415 (mp0) cc_final: 0.8100 (mp0) REVERT: A 105 ARG cc_start: 0.8516 (ttp80) cc_final: 0.7883 (ttp-170) REVERT: B 105 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7850 (mtm110) REVERT: B 109 LYS cc_start: 0.8343 (mmpt) cc_final: 0.8137 (mmmt) REVERT: C 98 GLU cc_start: 0.8404 (mp0) cc_final: 0.8122 (mp0) REVERT: C 105 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7846 (ttm-80) REVERT: D 98 GLU cc_start: 0.8410 (mp0) cc_final: 0.8074 (mp0) REVERT: D 399 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7585 (tp30) REVERT: E 105 ARG cc_start: 0.8482 (ttp80) cc_final: 0.7835 (ttp-170) REVERT: E 109 LYS cc_start: 0.8334 (mmpt) cc_final: 0.8124 (mmmt) REVERT: F 98 GLU cc_start: 0.8406 (mp0) cc_final: 0.8123 (mp0) REVERT: F 105 ARG cc_start: 0.8472 (ttp80) cc_final: 0.7838 (ttm-80) REVERT: G 98 GLU cc_start: 0.8415 (mp0) cc_final: 0.8083 (mp0) REVERT: G 105 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7920 (ttp-170) REVERT: H 105 ARG cc_start: 0.8504 (ttp80) cc_final: 0.7954 (ttp-170) outliers start: 47 outliers final: 32 residues processed: 423 average time/residue: 1.7677 time to fit residues: 832.5861 Evaluate side-chains 410 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 378 time to evaluate : 2.751 ------------------------------------------------------------------------------- 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 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 107 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 GLN A 498 GLN B 498 GLN C 498 GLN D 21 GLN D 441 GLN D 498 GLN E 441 GLN E 498 GLN F 498 GLN G 498 GLN H 441 GLN H 498 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.095380 restraints weight = 20146.477| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.18 r_work: 0.2912 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 24072 Z= 0.299 Angle : 0.752 6.185 32568 Z= 0.420 Chirality : 0.056 0.365 3712 Planarity : 0.005 0.031 4120 Dihedral : 10.770 119.250 3840 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.84 % Allowed : 8.62 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3024 helix: 0.75 (0.14), residues: 1240 sheet: -0.60 (0.24), residues: 384 loop : -0.10 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 466 PHE 0.018 0.004 PHE F 24 TYR 0.022 0.003 TYR F 4 ARG 0.005 0.001 ARG E 341 Details of bonding type rmsd hydrogen bonds : bond 0.08145 ( 1022) hydrogen bonds : angle 5.95882 ( 2859) covalent geometry : bond 0.00674 (24064) covalent geometry : angle 0.75152 (32568) Misc. bond : bond 0.00039 ( 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 429 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 384 time to evaluate : 2.859 Fit side-chains REVERT: B 98 GLU cc_start: 0.8428 (mp0) cc_final: 0.8100 (mp0) REVERT: B 105 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7849 (mtm110) REVERT: C 98 GLU cc_start: 0.8437 (mp0) cc_final: 0.8164 (mp0) REVERT: D 98 GLU cc_start: 0.8442 (mp0) cc_final: 0.8085 (mp0) REVERT: D 399 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7603 (tp30) REVERT: E 105 ARG cc_start: 0.8436 (ttp80) cc_final: 0.7888 (mtm110) REVERT: G 98 GLU cc_start: 0.8440 (mp0) cc_final: 0.8087 (mp0) REVERT: H 105 ARG cc_start: 0.8457 (ttp80) cc_final: 0.7900 (ttp-170) outliers start: 45 outliers final: 29 residues processed: 423 average time/residue: 1.8102 time to fit residues: 850.4630 Evaluate side-chains 403 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 374 time to evaluate : 2.777 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 303 optimal weight: 0.3980 chunk 250 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 216 optimal weight: 0.1980 chunk 158 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099916 restraints weight = 20145.314| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.18 r_work: 0.2980 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24072 Z= 0.110 Angle : 0.495 4.206 32568 Z= 0.279 Chirality : 0.041 0.143 3712 Planarity : 0.004 0.033 4120 Dihedral : 10.032 99.530 3840 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.00 % Allowed : 8.42 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3024 helix: 1.64 (0.15), residues: 1240 sheet: -0.24 (0.24), residues: 384 loop : 0.15 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 466 PHE 0.010 0.002 PHE H 401 TYR 0.009 0.001 TYR H 353 ARG 0.002 0.000 ARG F 512 Details of bonding type rmsd hydrogen bonds : bond 0.04967 ( 1022) hydrogen bonds : angle 5.30951 ( 2859) covalent geometry : bond 0.00221 (24064) covalent geometry : angle 0.49466 (32568) Misc. bond : bond 0.00004 ( 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 423 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 374 time to evaluate : 2.760 Fit side-chains REVERT: A 105 ARG cc_start: 0.8495 (ttp80) cc_final: 0.7862 (ttp-170) REVERT: B 98 GLU cc_start: 0.8381 (mp0) cc_final: 0.8123 (mp0) REVERT: B 105 ARG cc_start: 0.8475 (ttp80) cc_final: 0.7951 (mtm110) REVERT: C 450 LYS cc_start: 0.8423 (mttp) cc_final: 0.8143 (mttp) REVERT: D 98 GLU cc_start: 0.8409 (mp0) cc_final: 0.8133 (mp0) REVERT: D 399 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7569 (tp30) REVERT: D 450 LYS cc_start: 0.8465 (mttp) cc_final: 0.8163 (mttp) REVERT: E 105 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7875 (ttp-170) REVERT: F 450 LYS cc_start: 0.8427 (mttp) cc_final: 0.8136 (mttp) REVERT: G 98 GLU cc_start: 0.8412 (mp0) cc_final: 0.8139 (mp0) REVERT: H 105 ARG cc_start: 0.8505 (ttp80) cc_final: 0.7836 (ttp-170) outliers start: 49 outliers final: 27 residues processed: 418 average time/residue: 1.7696 time to fit residues: 823.3039 Evaluate side-chains 394 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 367 time to evaluate : 2.446 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 264 optimal weight: 0.9990 chunk 163 optimal weight: 0.0060 chunk 104 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 290 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 21 GLN H 265 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.098789 restraints weight = 20264.196| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.19 r_work: 0.2963 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24072 Z= 0.130 Angle : 0.528 4.300 32568 Z= 0.296 Chirality : 0.043 0.147 3712 Planarity : 0.004 0.032 4120 Dihedral : 10.053 102.532 3840 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.51 % Allowed : 9.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.15), residues: 3024 helix: 1.60 (0.15), residues: 1240 sheet: -0.20 (0.24), residues: 384 loop : 0.18 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 466 PHE 0.012 0.002 PHE H 401 TYR 0.011 0.002 TYR A 348 ARG 0.002 0.000 ARG E 480 Details of bonding type rmsd hydrogen bonds : bond 0.05537 ( 1022) hydrogen bonds : angle 5.38503 ( 2859) covalent geometry : bond 0.00272 (24064) covalent geometry : angle 0.52758 (32568) Misc. bond : bond 0.00009 ( 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 411 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 374 time to evaluate : 2.923 Fit side-chains REVERT: A 105 ARG cc_start: 0.8492 (ttp80) cc_final: 0.7879 (ttp-170) REVERT: B 98 GLU cc_start: 0.8381 (mp0) cc_final: 0.8118 (mp0) REVERT: B 105 ARG cc_start: 0.8503 (ttp80) cc_final: 0.7894 (ttp-170) REVERT: C 450 LYS cc_start: 0.8425 (mttp) cc_final: 0.8143 (mttp) REVERT: D 98 GLU cc_start: 0.8409 (mp0) cc_final: 0.8147 (mp0) REVERT: D 399 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7592 (tp30) REVERT: D 450 LYS cc_start: 0.8456 (mttp) cc_final: 0.8173 (mttp) REVERT: E 105 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7894 (ttp-170) REVERT: F 98 GLU cc_start: 0.8373 (mp0) cc_final: 0.8124 (mp0) REVERT: F 450 LYS cc_start: 0.8432 (mttp) cc_final: 0.8148 (mttp) REVERT: G 98 GLU cc_start: 0.8407 (mp0) cc_final: 0.8149 (mp0) REVERT: H 105 ARG cc_start: 0.8508 (ttp80) cc_final: 0.7891 (ttp-170) outliers start: 37 outliers final: 27 residues processed: 408 average time/residue: 1.8392 time to fit residues: 836.0498 Evaluate side-chains 392 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 365 time to evaluate : 2.475 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 178 optimal weight: 0.0170 chunk 105 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 193 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN B 368 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 21 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.121099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097558 restraints weight = 20106.628| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.18 r_work: 0.2945 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.0856 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= 0.165 Angle : 0.584 4.600 32568 Z= 0.327 Chirality : 0.045 0.184 3712 Planarity : 0.004 0.031 4120 Dihedral : 10.269 112.417 3840 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.31 % Allowed : 9.97 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3024 helix: 1.42 (0.15), residues: 1240 sheet: -0.27 (0.24), residues: 384 loop : 0.11 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.014 0.002 PHE H 401 TYR 0.014 0.002 TYR B 4 ARG 0.002 0.000 ARG F 512 Details of bonding type rmsd hydrogen bonds : bond 0.06242 ( 1022) hydrogen bonds : angle 5.55967 ( 2859) covalent geometry : bond 0.00357 (24064) covalent geometry : angle 0.58355 (32568) Misc. bond : bond 0.00017 ( 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 394 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 2.528 Fit side-chains REVERT: A 105 ARG cc_start: 0.8471 (ttp80) cc_final: 0.7884 (ttp-170) REVERT: C 450 LYS cc_start: 0.8413 (mttp) cc_final: 0.8147 (mttp) REVERT: D 98 GLU cc_start: 0.8414 (mp0) cc_final: 0.8110 (mp0) REVERT: D 399 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7588 (tp30) REVERT: F 98 GLU cc_start: 0.8394 (mp0) cc_final: 0.8096 (mp0) REVERT: F 450 LYS cc_start: 0.8412 (mttp) cc_final: 0.8137 (mttp) REVERT: G 98 GLU cc_start: 0.8410 (mp0) cc_final: 0.8107 (mp0) REVERT: H 105 ARG cc_start: 0.8512 (ttp80) cc_final: 0.7914 (ttp-170) outliers start: 32 outliers final: 27 residues processed: 390 average time/residue: 1.8010 time to fit residues: 789.9319 Evaluate side-chains 394 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 367 time to evaluate : 2.584 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 157 optimal weight: 4.9990 chunk 267 optimal weight: 0.0970 chunk 38 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 184 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.097039 restraints weight = 20178.559| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.19 r_work: 0.2935 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24072 Z= 0.188 Angle : 0.613 4.956 32568 Z= 0.344 Chirality : 0.047 0.213 3712 Planarity : 0.004 0.030 4120 Dihedral : 10.352 114.833 3840 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.63 % Allowed : 9.72 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3024 helix: 1.28 (0.15), residues: 1240 sheet: -0.32 (0.24), residues: 384 loop : 0.07 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 466 PHE 0.015 0.003 PHE H 401 TYR 0.015 0.002 TYR G 4 ARG 0.004 0.001 ARG H 341 Details of bonding type rmsd hydrogen bonds : bond 0.06582 ( 1022) hydrogen bonds : angle 5.63548 ( 2859) covalent geometry : bond 0.00412 (24064) covalent geometry : angle 0.61341 (32568) Misc. bond : bond 0.00006 ( 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 407 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 367 time to evaluate : 2.518 Fit side-chains REVERT: A 105 ARG cc_start: 0.8519 (ttp80) cc_final: 0.7899 (ttp-170) REVERT: B 98 GLU cc_start: 0.8413 (mp0) cc_final: 0.8146 (mp0) REVERT: C 450 LYS cc_start: 0.8423 (mttp) cc_final: 0.8132 (mttp) REVERT: D 98 GLU cc_start: 0.8433 (mp0) cc_final: 0.8100 (mp0) REVERT: D 399 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7593 (tp30) REVERT: F 450 LYS cc_start: 0.8433 (mttp) cc_final: 0.8161 (mttp) REVERT: H 105 ARG cc_start: 0.8492 (ttp80) cc_final: 0.7901 (ttp-170) outliers start: 40 outliers final: 27 residues processed: 405 average time/residue: 1.8689 time to fit residues: 840.9968 Evaluate side-chains 395 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 218 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 216 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN B 265 GLN C 265 GLN D 21 GLN D 265 GLN E 265 GLN F 265 GLN G 265 GLN H 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098077 restraints weight = 20258.538| |-----------------------------------------------------------------------------| 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: 0.8988 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24072 Z= 0.152 Angle : 0.561 4.494 32568 Z= 0.316 Chirality : 0.044 0.151 3712 Planarity : 0.004 0.031 4120 Dihedral : 10.221 109.973 3840 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.35 % Allowed : 9.84 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 3024 helix: 1.43 (0.15), residues: 1240 sheet: -0.26 (0.24), residues: 384 loop : 0.11 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 466 PHE 0.012 0.002 PHE D 401 TYR 0.012 0.002 TYR F 348 ARG 0.003 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.05900 ( 1022) hydrogen bonds : angle 5.53410 ( 2859) covalent geometry : bond 0.00325 (24064) covalent geometry : angle 0.56116 (32568) Misc. bond : bond 0.00006 ( 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 389 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 356 time to evaluate : 3.050 Fit side-chains REVERT: A 105 ARG cc_start: 0.8475 (ttp80) cc_final: 0.7892 (ttp-170) REVERT: B 98 GLU cc_start: 0.8401 (mp0) cc_final: 0.8131 (mp0) REVERT: B 105 ARG cc_start: 0.8513 (ttp80) cc_final: 0.7925 (ttp-170) REVERT: C 450 LYS cc_start: 0.8411 (mttp) cc_final: 0.8150 (mttp) REVERT: D 98 GLU cc_start: 0.8422 (mp0) cc_final: 0.8085 (mp0) REVERT: D 399 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7590 (tp30) REVERT: E 105 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7904 (ttp-170) REVERT: F 450 LYS cc_start: 0.8407 (mttp) cc_final: 0.8137 (mttp) REVERT: H 105 ARG cc_start: 0.8507 (ttp80) cc_final: 0.7891 (ttp-170) outliers start: 33 outliers final: 27 residues processed: 389 average time/residue: 1.7542 time to fit residues: 760.6385 Evaluate side-chains 382 residues out of total 2448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 355 time to evaluate : 2.443 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096455 restraints weight = 20136.970| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.18 r_work: 0.2927 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24072 Z= 0.229 Angle : 0.674 5.526 32568 Z= 0.377 Chirality : 0.050 0.272 3712 Planarity : 0.005 0.030 4120 Dihedral : 10.477 117.013 3840 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.35 % Allowed : 9.89 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.27 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3024 helix: 1.07 (0.14), residues: 1240 sheet: -0.41 (0.24), residues: 384 loop : 0.01 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 466 PHE 0.017 0.003 PHE G 401 TYR 0.018 0.003 TYR H 4 ARG 0.005 0.001 ARG E 341 Details of bonding type rmsd hydrogen bonds : bond 0.07215 ( 1022) hydrogen bonds : angle 5.76440 ( 2859) covalent geometry : bond 0.00509 (24064) covalent geometry : angle 0.67405 (32568) Misc. bond : bond 0.00013 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23119.99 seconds wall clock time: 399 minutes 37.99 seconds (23977.99 seconds total)