Starting phenix.real_space_refine on Fri Jun 5 18:01:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8y_42029/06_2026/8u8y_42029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8y_42029/06_2026/8u8y_42029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8y_42029/06_2026/8u8y_42029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8y_42029/06_2026/8u8y_42029.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8y_42029/06_2026/8u8y_42029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8y_42029/06_2026/8u8y_42029.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.074 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 160 5.16 5 C 14208 2.51 5 N 3840 2.21 5 O 4384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 109 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22616 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "B" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "C" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "D" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "E" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "F" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "G" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "H" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2760 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 11, 'TRANS': 355} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 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: {'IMP%rna3p': 1, 'NAD': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 5.68, per 1000 atoms: 0.25 Number of scatterers: 22616 At special positions: 0 Unit cell: (117.177, 117.177, 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 160 16.00 P 24 15.00 O 4384 8.00 N 3840 7.00 C 14208 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=0, symmetry=0 Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5232 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 44.3% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... 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 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.675A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' 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 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 86 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.269A 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: 3.675A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' 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 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 86 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.285A 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: 3.674A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' 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 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 86 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.279A 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: 3.675A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 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 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 86 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 254 through 267 removed outlier: 4.283A 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: 3.674A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 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 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 86 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.284A 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: 3.675A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 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 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 86 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 255 through 267 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.675A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' 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 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 86 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.675A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 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: 3.584A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.794A pdb=" N SER A 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.842A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 444 " --> pdb=" O THR A 510 " (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: 3.586A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.841A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER C 444 " --> pdb=" O THR B 510 " (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: 3.586A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY C 302 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU C 273 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N VAL C 304 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.841A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER D 444 " --> pdb=" O THR 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: 3.585A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (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: 3.586A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.800A pdb=" N SER E 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.842A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER F 444 " --> pdb=" O THR E 510 " (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: 3.584A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N GLY F 302 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.842A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER G 444 " --> pdb=" O THR 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: 3.585A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLY G 302 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.842A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER H 444 " --> pdb=" O THR G 510 " (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: 3.584A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY H 302 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) 944 hydrogen bonds defined for protein. 2640 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 2.51 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: 3776 1.30 - 1.43: 5771 1.43 - 1.56: 13149 1.56 - 1.69: 40 1.69 - 1.82: 272 Bond restraints: 23008 Sorted by residual: bond pdb=" C2 IMP E 601 " pdb=" N3 IMP E 601 " ideal model delta sigma weight residual 1.301 1.454 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C2 IMP H 601 " pdb=" N3 IMP H 601 " ideal model delta sigma weight residual 1.301 1.454 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C2 IMP F 601 " pdb=" N3 IMP F 601 " ideal model delta sigma weight residual 1.301 1.454 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C2 IMP A 601 " pdb=" N3 IMP A 601 " ideal model delta sigma weight residual 1.301 1.454 -0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C2 IMP C 601 " pdb=" N3 IMP C 601 " ideal model delta sigma weight residual 1.301 1.454 -0.153 2.00e-02 2.50e+03 5.86e+01 ... (remaining 23003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 30146 1.98 - 3.97: 788 3.97 - 5.95: 138 5.95 - 7.94: 40 7.94 - 9.92: 24 Bond angle restraints: 31136 Sorted by residual: angle pdb=" C5 IMP D 601 " pdb=" C6 IMP D 601 " pdb=" N1 IMP D 601 " ideal model delta sigma weight residual 110.14 120.06 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C5 IMP E 601 " pdb=" C6 IMP E 601 " pdb=" N1 IMP E 601 " ideal model delta sigma weight residual 110.14 120.06 -9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C5 IMP A 601 " pdb=" C6 IMP A 601 " pdb=" N1 IMP A 601 " ideal model delta sigma weight residual 110.14 120.05 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C5 IMP B 601 " pdb=" C6 IMP B 601 " pdb=" N1 IMP B 601 " ideal model delta sigma weight residual 110.14 120.01 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C5 IMP F 601 " pdb=" C6 IMP F 601 " pdb=" N1 IMP F 601 " ideal model delta sigma weight residual 110.14 120.01 -9.87 3.00e+00 1.11e-01 1.08e+01 ... (remaining 31131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 12181 17.42 - 34.83: 1345 34.83 - 52.25: 415 52.25 - 69.66: 83 69.66 - 87.08: 48 Dihedral angle restraints: 14072 sinusoidal: 5816 harmonic: 8256 Sorted by residual: dihedral pdb=" CA THR E 74 " pdb=" C THR E 74 " pdb=" N GLU E 75 " pdb=" CA GLU E 75 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR A 74 " pdb=" C THR A 74 " pdb=" N GLU A 75 " pdb=" CA GLU A 75 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR F 74 " pdb=" C THR F 74 " pdb=" N GLU F 75 " pdb=" CA GLU F 75 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 14069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1999 0.032 - 0.064: 1012 0.064 - 0.096: 311 0.096 - 0.129: 167 0.129 - 0.161: 71 Chirality restraints: 3560 Sorted by residual: chirality pdb=" CA ILE G 447 " pdb=" N ILE G 447 " pdb=" C ILE G 447 " pdb=" CB ILE G 447 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE D 447 " pdb=" N ILE D 447 " pdb=" C ILE D 447 " pdb=" CB ILE D 447 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ILE B 447 " pdb=" N ILE B 447 " pdb=" C ILE B 447 " pdb=" CB ILE B 447 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 3557 not shown) Planarity restraints: 3936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 457 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO H 458 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 458 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 458 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 457 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO G 458 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 458 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 458 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 457 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 458 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.024 5.00e-02 4.00e+02 ... (remaining 3933 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7023 2.84 - 3.36: 21145 3.36 - 3.87: 39378 3.87 - 4.39: 47738 4.39 - 4.90: 75403 Nonbonded interactions: 190687 Sorted by model distance: nonbonded pdb=" OE1 GLN A 283 " pdb=" N GLY A 302 " model vdw 2.328 3.120 nonbonded pdb=" OE1 GLN C 283 " pdb=" N GLY C 302 " model vdw 2.329 3.120 nonbonded pdb=" OE1 GLN E 283 " pdb=" N GLY E 302 " model vdw 2.329 3.120 nonbonded pdb=" OE1 GLN B 283 " pdb=" N GLY B 302 " model vdw 2.329 3.120 nonbonded pdb=" OE1 GLN H 283 " pdb=" N GLY H 302 " model vdw 2.330 3.120 ... (remaining 190682 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: 0.08 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: 5.000 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.420 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.007 0.153 23008 Z= 0.359 Angle : 0.839 9.922 31136 Z= 0.417 Chirality : 0.048 0.161 3560 Planarity : 0.005 0.048 3936 Dihedral : 17.065 87.081 8840 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.76 % Allowed : 14.30 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.15), residues: 2888 helix: 1.24 (0.14), residues: 1224 sheet: -0.26 (0.32), residues: 248 loop : -0.46 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 322 TYR 0.010 0.002 TYR B 353 PHE 0.014 0.002 PHE E 357 HIS 0.004 0.001 HIS H 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.36 (23008) covalent geometry : angle 0.83877 / 0.42 (31136) hydrogen bonds : bond 0.14401 / 9.30 ( 944) hydrogen bonds : angle 5.86844 / 4.25 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 0.796 Fit side-chains REVERT: A 109 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7815 (pttm) REVERT: B 109 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7811 (pttm) REVERT: C 109 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7816 (pttm) REVERT: D 109 LYS cc_start: 0.8052 (ptmt) cc_final: 0.7823 (pttm) REVERT: E 109 LYS cc_start: 0.8060 (ptmt) cc_final: 0.7816 (pttm) REVERT: F 109 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7817 (pttm) REVERT: G 109 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7813 (pttm) REVERT: H 109 LYS cc_start: 0.8057 (ptmt) cc_final: 0.7812 (pttm) outliers start: 41 outliers final: 33 residues processed: 372 average time/residue: 0.9031 time to fit residues: 370.6309 Evaluate side-chains 368 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 335 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 330 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0370 chunk 111 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 112 GLN B 94 ASN C 94 ASN C 368 GLN D 94 ASN D 112 GLN E 94 ASN F 94 ASN F 112 GLN G 94 ASN G 368 GLN H 94 ASN H 112 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.132980 restraints weight = 15746.523| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 0.83 r_work: 0.3348 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 23008 Z= 0.096 Angle : 0.469 4.246 31136 Z= 0.258 Chirality : 0.041 0.131 3560 Planarity : 0.003 0.035 3936 Dihedral : 10.214 70.385 3856 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.23 % Allowed : 13.14 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 2888 helix: 1.96 (0.15), residues: 1224 sheet: -0.05 (0.36), residues: 232 loop : -0.22 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 57 TYR 0.006 0.001 TYR G 353 PHE 0.007 0.001 PHE E 490 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.10 (23008) covalent geometry : angle 0.46940 / 0.26 (31136) hydrogen bonds : bond 0.04069 / 2.70 ( 944) hydrogen bonds : angle 5.00486 / 3.57 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 367 time to evaluate : 0.878 Fit side-chains REVERT: A 111 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6665 (mm-30) REVERT: B 111 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: C 111 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6646 (mm-30) REVERT: D 111 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: D 444 SER cc_start: 0.8887 (t) cc_final: 0.8610 (m) REVERT: E 111 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6674 (mm-30) REVERT: F 111 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: G 111 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6635 (mm-30) REVERT: H 111 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6677 (mm-30) outliers start: 52 outliers final: 20 residues processed: 406 average time/residue: 0.8138 time to fit residues: 367.8709 Evaluate side-chains 370 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 342 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 25 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 263 optimal weight: 0.3980 chunk 95 optimal weight: 0.0980 chunk 169 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 281 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN C 94 ASN D 94 ASN D 292 GLN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.130870 restraints weight = 15567.085| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 0.89 r_work: 0.3322 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23008 Z= 0.109 Angle : 0.490 4.461 31136 Z= 0.268 Chirality : 0.042 0.128 3560 Planarity : 0.003 0.035 3936 Dihedral : 9.170 64.801 3800 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.18 % Allowed : 13.18 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.15), residues: 2888 helix: 2.06 (0.15), residues: 1224 sheet: 0.01 (0.35), residues: 232 loop : -0.24 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.006 0.001 TYR B 353 PHE 0.009 0.001 PHE H 490 HIS 0.002 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (23008) covalent geometry : angle 0.49022 / 0.27 (31136) hydrogen bonds : bond 0.04565 / 3.03 ( 944) hydrogen bonds : angle 4.83774 / 3.45 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 362 time to evaluate : 0.899 Fit side-chains REVERT: F 444 SER cc_start: 0.8811 (t) cc_final: 0.8581 (m) outliers start: 51 outliers final: 33 residues processed: 400 average time/residue: 0.8196 time to fit residues: 365.7294 Evaluate side-chains 384 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 351 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 260 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 262 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 292 GLN C 94 ASN C 265 GLN D 94 ASN D 265 GLN D 292 GLN E 94 ASN E 265 GLN E 292 GLN F 94 ASN F 265 GLN F 292 GLN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123885 restraints weight = 15310.704| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.89 r_work: 0.3230 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23008 Z= 0.265 Angle : 0.790 6.916 31136 Z= 0.426 Chirality : 0.054 0.150 3560 Planarity : 0.006 0.055 3936 Dihedral : 9.027 57.953 3776 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.00 % Allowed : 11.90 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 2888 helix: 1.68 (0.15), residues: 1224 sheet: 0.01 (0.32), residues: 248 loop : -0.31 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 322 TYR 0.013 0.003 TYR B 353 PHE 0.017 0.003 PHE A 357 HIS 0.005 0.002 HIS E 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.27 (23008) covalent geometry : angle 0.78988 / 0.43 (31136) hydrogen bonds : bond 0.07763 / 5.14 ( 944) hydrogen bonds : angle 5.32505 / 3.79 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 343 time to evaluate : 0.826 Fit side-chains REVERT: A 111 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6869 (mm-30) REVERT: B 111 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6854 (mm-30) REVERT: C 111 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6899 (mm-30) REVERT: D 111 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: E 111 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6875 (mm-30) REVERT: F 111 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: G 111 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6875 (mm-30) REVERT: H 111 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6880 (mm-30) outliers start: 70 outliers final: 44 residues processed: 396 average time/residue: 0.8418 time to fit residues: 369.9437 Evaluate side-chains 390 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 4.9990 chunk 215 optimal weight: 0.4980 chunk 188 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN B 292 GLN C 94 ASN D 94 ASN D 265 GLN D 292 GLN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.154545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127806 restraints weight = 15309.636| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 0.88 r_work: 0.3282 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23008 Z= 0.138 Angle : 0.565 5.568 31136 Z= 0.309 Chirality : 0.044 0.130 3560 Planarity : 0.004 0.038 3936 Dihedral : 8.589 58.675 3776 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.95 % Allowed : 12.03 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 2888 helix: 1.92 (0.15), residues: 1224 sheet: 0.35 (0.31), residues: 288 loop : -0.33 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 57 TYR 0.008 0.001 TYR A 353 PHE 0.011 0.002 PHE C 490 HIS 0.003 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (23008) covalent geometry : angle 0.56509 / 0.31 (31136) hydrogen bonds : bond 0.05340 / 3.54 ( 944) hydrogen bonds : angle 5.01755 / 3.57 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 350 time to evaluate : 0.804 Fit side-chains REVERT: A 111 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: B 111 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6685 (mm-30) REVERT: C 111 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: D 111 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: D 444 SER cc_start: 0.8851 (t) cc_final: 0.8595 (m) REVERT: E 111 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: F 111 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: F 444 SER cc_start: 0.8845 (t) cc_final: 0.8605 (m) REVERT: G 111 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6723 (mm-30) REVERT: H 111 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6708 (mm-30) outliers start: 69 outliers final: 38 residues processed: 412 average time/residue: 0.8361 time to fit residues: 382.3878 Evaluate side-chains 394 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 348 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7001 > 50: distance: 13 - 38: 35.248 distance: 16 - 35: 33.663 distance: 30 - 35: 31.935 distance: 35 - 36: 19.558 distance: 36 - 37: 45.783 distance: 36 - 39: 46.169 distance: 37 - 38: 39.554 distance: 39 - 40: 11.281 distance: 40 - 41: 57.218 distance: 40 - 42: 10.175 distance: 43 - 44: 33.908 distance: 44 - 45: 56.759 distance: 44 - 47: 5.608 distance: 45 - 52: 40.285 distance: 48 - 49: 40.766 distance: 49 - 50: 56.911 distance: 50 - 51: 57.017 distance: 52 - 53: 39.594 distance: 53 - 56: 40.452 distance: 54 - 59: 53.566 distance: 56 - 57: 52.638 distance: 56 - 58: 4.480 distance: 59 - 60: 3.315 distance: 59 - 65: 38.214 distance: 60 - 61: 43.580 distance: 60 - 63: 44.651 distance: 61 - 62: 41.349 distance: 61 - 66: 43.665 distance: 63 - 64: 23.516 distance: 64 - 65: 41.182 distance: 66 - 67: 24.672 distance: 67 - 68: 51.860 distance: 67 - 70: 29.767 distance: 68 - 69: 41.240 distance: 68 - 74: 32.126 distance: 69 - 151: 32.811 distance: 70 - 71: 50.249 distance: 71 - 72: 7.492 distance: 74 - 75: 56.700 distance: 75 - 76: 12.855 distance: 75 - 78: 49.425 distance: 76 - 82: 56.573 distance: 78 - 79: 40.374 distance: 78 - 80: 40.625 distance: 79 - 81: 57.065 distance: 82 - 154: 35.274 distance: 83 - 84: 38.954 distance: 84 - 85: 39.704 distance: 86 - 87: 40.294 distance: 88 - 89: 17.294 distance: 89 - 90: 61.941 distance: 89 - 92: 59.731 distance: 94 - 95: 20.676 distance: 95 - 96: 20.825 distance: 95 - 98: 34.907 distance: 96 - 97: 40.824 distance: 99 - 100: 39.697 distance: 101 - 102: 55.488 distance: 102 - 103: 39.899 distance: 102 - 105: 41.481 distance: 103 - 109: 35.490 distance: 106 - 107: 39.938