Starting phenix.real_space_refine on Fri Aug 7 16:23:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u8y_42029/08_2026/8u8y_42029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8y_42029/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8u8y_42029/08_2026/8u8y_42029.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u8y_42029/08_2026/8u8y_42029.cif" model { file = "/net/cci-nas-00/data/ceres_data/8u8y_42029/08_2026/8u8y_42029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8y_42029/08_2026/8u8y_42029.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u8y_42029/08_2026/8u8y_42029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8y_42029/08_2026/8u8y_42029.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 4.40, per 1000 atoms: 0.19 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: 1.86 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: 0.79 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: 4.49 Time building geometry restraints manager: 2.47 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=" C5 IMP H 601 " pdb=" C6 IMP H 601 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C5 IMP B 601 " pdb=" C6 IMP B 601 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C5 IMP G 601 " pdb=" C6 IMP G 601 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C5 IMP C 601 " pdb=" C6 IMP C 601 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C5 IMP F 601 " pdb=" C6 IMP F 601 " ideal model delta sigma weight residual 1.390 1.534 -0.144 2.00e-02 2.50e+03 5.19e+01 ... (remaining 23003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 30070 1.84 - 3.67: 880 3.67 - 5.51: 154 5.51 - 7.34: 8 7.34 - 9.18: 24 Bond angle restraints: 31136 Sorted by residual: angle pdb=" N GLN D 265 " pdb=" CA GLN D 265 " pdb=" C GLN D 265 " ideal model delta sigma weight residual 112.23 108.13 4.10 1.26e+00 6.30e-01 1.06e+01 angle pdb=" N GLN E 265 " pdb=" CA GLN E 265 " pdb=" C GLN E 265 " ideal model delta sigma weight residual 111.82 108.23 3.59 1.16e+00 7.43e-01 9.56e+00 angle pdb=" C1' IMP E 601 " pdb=" C2' IMP E 601 " pdb=" C3' IMP E 601 " ideal model delta sigma weight residual 111.00 101.82 9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" C1' IMP H 601 " pdb=" C2' IMP H 601 " pdb=" C3' IMP H 601 " ideal model delta sigma weight residual 111.00 101.83 9.17 3.00e+00 1.11e-01 9.34e+00 angle pdb=" C1' IMP C 601 " pdb=" C2' IMP C 601 " pdb=" C3' IMP C 601 " ideal model delta sigma weight residual 111.00 101.84 9.16 3.00e+00 1.11e-01 9.32e+00 ... (remaining 31131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.24: 12727 23.24 - 46.47: 958 46.47 - 69.71: 207 69.71 - 92.94: 48 92.94 - 116.18: 4 Dihedral angle restraints: 13944 sinusoidal: 5688 harmonic: 8256 Sorted by residual: dihedral pdb=" C5' IMP E 601 " pdb=" O5' IMP E 601 " pdb=" P IMP E 601 " pdb=" O2P IMP E 601 " ideal model delta sinusoidal sigma weight residual 191.93 75.75 116.18 1 2.00e+01 2.50e-03 3.46e+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 75.81 116.12 1 2.00e+01 2.50e-03 3.46e+01 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 75.87 116.07 1 2.00e+01 2.50e-03 3.45e+01 ... (remaining 13941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2664 0.051 - 0.103: 703 0.103 - 0.154: 172 0.154 - 0.205: 13 0.205 - 0.256: 8 Chirality restraints: 3560 Sorted by residual: chirality pdb=" C2' IMP E 601 " pdb=" C1' IMP E 601 " pdb=" C3' IMP E 601 " pdb=" O2' IMP E 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2' IMP H 601 " pdb=" C1' IMP H 601 " pdb=" C3' IMP H 601 " pdb=" O2' IMP H 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" C2' IMP F 601 " pdb=" C1' IMP F 601 " pdb=" C3' IMP F 601 " pdb=" O2' IMP F 601 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.25 2.00e-01 2.50e+01 1.61e+00 ... (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: 0.09 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: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.930 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 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 0.144 23008 Z= 0.335 Angle : 0.797 9.181 31136 Z= 0.407 Chirality : 0.049 0.256 3560 Planarity : 0.005 0.048 3936 Dihedral : 17.234 116.178 8712 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 0.00669 / 0.33 (23008) covalent geometry : angle 0.79668 / 0.41 (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 : 0.791 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: 0.8137 time to fit residues: 335.9856 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 : 0.886 ------------------------------------------------------------------------------- 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... A 94 ASN A 112 GLN A 368 GLN B 94 ASN B 368 GLN C 94 ASN C 368 GLN D 94 ASN D 112 GLN D 368 GLN E 94 ASN E 368 GLN F 94 ASN F 112 GLN F 368 GLN G 94 ASN G 368 GLN H 94 ASN H 112 GLN H 368 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.159335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134017 restraints weight = 15767.049| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.83 r_work: 0.3353 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 23008 Z= 0.097 Angle : 0.502 7.406 31136 Z= 0.263 Chirality : 0.041 0.126 3560 Planarity : 0.003 0.034 3936 Dihedral : 10.436 89.214 3728 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.31 % Allowed : 12.97 % Favored : 84.72 % 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: 1.08 (0.16), residues: 2888 helix: 1.96 (0.15), residues: 1224 sheet: 0.26 (0.38), residues: 216 loop : -0.26 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 57 TYR 0.006 0.001 TYR F 353 PHE 0.006 0.001 PHE B 99 HIS 0.002 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.10 (23008) covalent geometry : angle 0.50245 / 0.26 (31136) hydrogen bonds : bond 0.03945 / 2.61 ( 944) hydrogen bonds : angle 5.00888 / 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 423 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 369 time to evaluate : 0.875 Fit side-chains REVERT: A 111 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6654 (mm-30) REVERT: B 111 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: C 111 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6614 (mm-30) REVERT: D 111 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6624 (mm-30) REVERT: D 444 SER cc_start: 0.8875 (t) cc_final: 0.8598 (m) REVERT: E 111 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: F 111 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: G 111 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6606 (mm-30) REVERT: H 111 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6648 (mm-30) outliers start: 54 outliers final: 15 residues processed: 408 average time/residue: 0.7361 time to fit residues: 336.0326 Evaluate side-chains 368 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 455 LYS 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 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 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: 10.0000 chunk 258 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 263 optimal weight: 0.0980 chunk 95 optimal weight: 0.0970 chunk 169 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 281 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3724 r_free = 0.3724 target = 0.156110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129325 restraints weight = 15520.619| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 0.89 r_work: 0.3302 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23008 Z= 0.125 Angle : 0.560 8.038 31136 Z= 0.294 Chirality : 0.043 0.130 3560 Planarity : 0.004 0.036 3936 Dihedral : 9.657 100.844 3672 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.74 % Allowed : 12.89 % Favored : 84.38 % 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: 1.09 (0.15), residues: 2888 helix: 2.00 (0.15), residues: 1224 sheet: 0.01 (0.36), residues: 232 loop : -0.25 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 57 TYR 0.007 0.001 TYR B 353 PHE 0.009 0.001 PHE B 490 HIS 0.002 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (23008) covalent geometry : angle 0.56013 / 0.29 (31136) hydrogen bonds : bond 0.05002 / 3.31 ( 944) hydrogen bonds : angle 4.92718 / 3.51 ( 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 421 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 357 time to evaluate : 0.912 Fit side-chains REVERT: A 111 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6525 (mm-30) REVERT: B 111 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: E 111 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6520 (mm-30) REVERT: F 444 SER cc_start: 0.8854 (t) cc_final: 0.8595 (m) REVERT: H 111 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6526 (mm-30) outliers start: 64 outliers final: 43 residues processed: 399 average time/residue: 0.7829 time to fit residues: 349.6374 Evaluate side-chains 399 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP 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 A residue 455 LYS 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 260 LEU 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 16 ASP Chi-restraints excluded: chain C residue 63 THR 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 C residue 455 LYS Chi-restraints excluded: chain D residue 16 ASP 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 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 E residue 455 LYS Chi-restraints excluded: chain F residue 16 ASP 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 16 ASP 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 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU 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: 4.9990 chunk 213 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 281 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 262 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN 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 G 292 GLN H 94 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124290 restraints weight = 15321.795| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.89 r_work: 0.3236 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23008 Z= 0.247 Angle : 0.789 8.617 31136 Z= 0.417 Chirality : 0.053 0.146 3560 Planarity : 0.006 0.052 3936 Dihedral : 9.882 112.331 3660 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.95 % Allowed : 11.82 % Favored : 85.23 % 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: 1.70 (0.15), residues: 1224 sheet: -0.05 (0.33), residues: 248 loop : -0.31 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 322 TYR 0.012 0.003 TYR H 353 PHE 0.016 0.003 PHE D 357 HIS 0.004 0.001 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.25 (23008) covalent geometry : angle 0.78927 / 0.42 (31136) hydrogen bonds : bond 0.07513 / 4.97 ( 944) hydrogen bonds : angle 5.29944 / 3.77 ( 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 411 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 342 time to evaluate : 0.879 Fit side-chains REVERT: C 111 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6876 (mm-30) REVERT: D 111 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6887 (mm-30) REVERT: F 111 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6871 (mm-30) REVERT: G 111 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6870 (mm-30) outliers start: 69 outliers final: 62 residues processed: 397 average time/residue: 0.7511 time to fit residues: 332.4227 Evaluate side-chains 405 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 339 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 A residue 410 LYS Chi-restraints excluded: chain A residue 455 LYS 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 260 LEU 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 B residue 410 LYS Chi-restraints excluded: chain B residue 455 LYS 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 C residue 410 LYS 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 D residue 410 LYS 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 E residue 410 LYS 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 F residue 410 LYS Chi-restraints excluded: chain F residue 455 LYS 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 G residue 410 LYS Chi-restraints excluded: chain G residue 455 LYS 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 Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 283 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 226 optimal weight: 0.0770 chunk 214 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN B 292 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 = 0.3718 r_free = 0.3718 target = 0.155507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128918 restraints weight = 15374.022| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.88 r_work: 0.3298 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.0872 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= 0.125 Angle : 0.568 7.914 31136 Z= 0.299 Chirality : 0.044 0.128 3560 Planarity : 0.004 0.038 3936 Dihedral : 9.279 102.295 3660 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: 1.11 (0.15), residues: 2888 helix: 1.98 (0.15), residues: 1224 sheet: 0.42 (0.32), residues: 288 loop : -0.31 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 57 TYR 0.007 0.001 TYR A 484 PHE 0.010 0.001 PHE C 490 HIS 0.002 0.001 HIS F 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (23008) covalent geometry : angle 0.56829 / 0.30 (31136) hydrogen bonds : bond 0.04934 / 3.27 ( 944) hydrogen bonds : angle 4.94481 / 3.53 ( 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 426 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 356 time to evaluate : 0.861 Fit side-chains REVERT: A 111 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6696 (mm-30) REVERT: B 111 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: C 111 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6643 (mm-30) REVERT: D 111 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6689 (mm-30) REVERT: D 444 SER cc_start: 0.8816 (t) cc_final: 0.8582 (m) REVERT: E 111 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: F 111 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6673 (mm-30) REVERT: F 444 SER cc_start: 0.8819 (t) cc_final: 0.8600 (m) REVERT: G 111 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6685 (mm-30) REVERT: H 111 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6698 (mm-30) outliers start: 70 outliers final: 44 residues processed: 414 average time/residue: 0.7615 time to fit residues: 352.1041 Evaluate side-chains 402 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 A residue 455 LYS 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 260 LEU 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 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 F residue 455 LYS 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 G residue 455 LYS 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 Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 101 optimal weight: 9.9990 chunk 241 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.7018 > 50:) chunk 254 optimal weight: 0.0670 chunk 146 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 5 optimal weight: 0.0010 overall best weight: 1.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN E 94 ASN E 265 GLN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130839 restraints weight = 15547.327| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.83 r_work: 0.3322 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23008 Z= 0.114 Angle : 0.539 7.794 31136 Z= 0.282 Chirality : 0.042 0.128 3560 Planarity : 0.003 0.037 3936 Dihedral : 8.920 98.162 3660 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.44 % Allowed : 12.80 % Favored : 84.76 % 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: 1.18 (0.15), residues: 2888 helix: 2.08 (0.15), residues: 1224 sheet: 0.46 (0.33), residues: 272 loop : -0.31 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 57 TYR 0.007 0.001 TYR E 353 PHE 0.009 0.001 PHE B 490 HIS 0.002 0.001 HIS C 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (23008) covalent geometry : angle 0.53940 / 0.28 (31136) hydrogen bonds : bond 0.04592 / 3.04 ( 944) hydrogen bonds : angle 4.79824 / 3.42 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 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 431 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 374 time to evaluate : 0.922 Fit side-chains REVERT: A 111 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: B 111 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6606 (mm-30) REVERT: C 111 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: D 111 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6664 (mm-30) REVERT: E 111 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: F 111 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6673 (mm-30) REVERT: G 111 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6661 (mm-30) REVERT: H 111 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6622 (mm-30) outliers start: 57 outliers final: 42 residues processed: 418 average time/residue: 0.7765 time to fit residues: 363.4987 Evaluate side-chains 407 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 357 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP 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 A residue 455 LYS 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 B residue 455 LYS 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 F residue 455 LYS 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 G residue 455 LYS 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 Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 55 optimal weight: 0.0870 chunk 65 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 195 optimal weight: 0.6980 chunk 277 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 176 optimal weight: 0.3980 chunk 159 optimal weight: 10.0000 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.155826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129063 restraints weight = 15432.327| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.89 r_work: 0.3299 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0967 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= 0.124 Angle : 0.564 8.030 31136 Z= 0.295 Chirality : 0.043 0.130 3560 Planarity : 0.004 0.037 3936 Dihedral : 8.990 102.133 3660 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.53 % Allowed : 13.57 % Favored : 83.90 % 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: 1.12 (0.15), residues: 2888 helix: 2.05 (0.15), residues: 1224 sheet: 0.35 (0.30), residues: 288 loop : -0.34 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 57 TYR 0.008 0.001 TYR A 353 PHE 0.009 0.001 PHE G 490 HIS 0.002 0.001 HIS B 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (23008) covalent geometry : angle 0.56411 / 0.30 (31136) hydrogen bonds : bond 0.04909 / 3.25 ( 944) hydrogen bonds : angle 4.84750 / 3.46 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 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 403 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 344 time to evaluate : 0.937 Fit side-chains REVERT: A 111 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: B 111 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6533 (mm-30) REVERT: C 111 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: D 111 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: E 111 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6541 (mm-30) REVERT: F 111 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6598 (mm-30) REVERT: G 111 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6590 (mm-30) REVERT: H 111 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6538 (mm-30) outliers start: 59 outliers final: 41 residues processed: 392 average time/residue: 0.7675 time to fit residues: 336.3014 Evaluate side-chains 392 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 343 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 A residue 455 LYS 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 B residue 455 LYS 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 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 330 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 455 LYS 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 G residue 455 LYS 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 Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.0030 chunk 183 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 226 optimal weight: 0.8980 chunk 280 optimal weight: 0.4980 chunk 64 optimal weight: 0.0770 chunk 137 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN C 94 ASN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.133941 restraints weight = 15584.994| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.88 r_work: 0.3363 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 23008 Z= 0.089 Angle : 0.483 7.319 31136 Z= 0.251 Chirality : 0.041 0.124 3560 Planarity : 0.003 0.035 3936 Dihedral : 8.320 89.401 3660 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.01 % Allowed : 14.21 % Favored : 83.78 % 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: 1.36 (0.16), residues: 2888 helix: 2.25 (0.15), residues: 1224 sheet: 0.51 (0.32), residues: 272 loop : -0.21 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 57 TYR 0.006 0.001 TYR E 353 PHE 0.008 0.001 PHE F 490 HIS 0.002 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.09 (23008) covalent geometry : angle 0.48288 / 0.25 (31136) hydrogen bonds : bond 0.03670 / 2.43 ( 944) hydrogen bonds : angle 4.60290 / 3.28 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 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 416 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 369 time to evaluate : 0.933 Fit side-chains REVERT: A 111 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6519 (mm-30) REVERT: B 111 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6482 (mm-30) REVERT: E 111 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6500 (mm-30) REVERT: H 111 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6529 (mm-30) outliers start: 47 outliers final: 26 residues processed: 404 average time/residue: 0.7891 time to fit residues: 356.3357 Evaluate side-chains 395 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 365 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 455 LYS 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 455 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 261 ASP 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 330 ILE 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 261 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 330 ILE 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 330 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 136 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 119 optimal weight: 0.0770 chunk 202 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 185 optimal weight: 0.0670 chunk 110 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN B 265 GLN C 94 ASN C 265 GLN D 94 ASN E 94 ASN F 94 ASN F 265 GLN G 94 ASN H 94 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.160066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133761 restraints weight = 15683.537| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 0.89 r_work: 0.3358 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 23008 Z= 0.092 Angle : 0.491 7.445 31136 Z= 0.253 Chirality : 0.041 0.125 3560 Planarity : 0.003 0.035 3936 Dihedral : 8.245 88.822 3660 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.84 % Allowed : 14.81 % Favored : 83.35 % 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: 1.40 (0.16), residues: 2888 helix: 2.28 (0.15), residues: 1224 sheet: 0.47 (0.31), residues: 272 loop : -0.18 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 57 TYR 0.007 0.001 TYR E 353 PHE 0.008 0.001 PHE D 490 HIS 0.002 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00180 / 0.09 (23008) covalent geometry : angle 0.49077 / 0.25 (31136) hydrogen bonds : bond 0.03746 / 2.49 ( 944) hydrogen bonds : angle 4.57767 / 3.27 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 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 398 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 355 time to evaluate : 1.194 Fit side-chains outliers start: 43 outliers final: 23 residues processed: 387 average time/residue: 0.7633 time to fit residues: 329.6607 Evaluate side-chains 375 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 352 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 330 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 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 203 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN B 265 GLN C 94 ASN C 265 GLN D 94 ASN E 94 ASN F 94 ASN F 265 GLN G 94 ASN H 94 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.153569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.126644 restraints weight = 15324.025| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 0.89 r_work: 0.3280 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23008 Z= 0.187 Angle : 0.679 8.393 31136 Z= 0.355 Chirality : 0.048 0.154 3560 Planarity : 0.005 0.037 3936 Dihedral : 8.898 110.164 3648 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.93 % Allowed : 14.51 % Favored : 83.56 % 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 (0.15), residues: 2888 helix: 1.96 (0.15), residues: 1224 sheet: 0.23 (0.34), residues: 232 loop : -0.28 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 407 TYR 0.010 0.002 TYR H 353 PHE 0.012 0.002 PHE H 99 HIS 0.003 0.001 HIS D 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (23008) covalent geometry : angle 0.67874 / 0.36 (31136) hydrogen bonds : bond 0.06130 / 4.06 ( 944) hydrogen bonds : angle 4.93941 / 3.52 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 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 394 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 349 time to evaluate : 0.836 Fit side-chains REVERT: C 111 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: D 111 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6617 (mm-30) REVERT: F 111 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6620 (mm-30) REVERT: G 111 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6609 (mm-30) outliers start: 45 outliers final: 21 residues processed: 377 average time/residue: 0.8019 time to fit residues: 337.1795 Evaluate side-chains 373 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 348 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 330 ILE 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 330 ILE Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 330 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 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 177 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 287 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN B 94 ASN B 265 GLN C 94 ASN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126190 restraints weight = 15295.909| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 0.88 r_work: 0.3263 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23008 Z= 0.188 Angle : 0.693 8.351 31136 Z= 0.364 Chirality : 0.049 0.159 3560 Planarity : 0.005 0.038 3936 Dihedral : 9.150 110.159 3648 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.16 % Allowed : 14.90 % 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: 0.94 (0.15), residues: 2888 helix: 1.81 (0.15), residues: 1224 sheet: 0.14 (0.32), residues: 248 loop : -0.30 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 407 TYR 0.010 0.002 TYR E 353 PHE 0.012 0.002 PHE E 99 HIS 0.003 0.001 HIS C 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (23008) covalent geometry : angle 0.69299 / 0.36 (31136) hydrogen bonds : bond 0.06310 / 4.18 ( 944) hydrogen bonds : angle 5.04585 / 3.60 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10185.63 seconds wall clock time: 173 minutes 41.39 seconds (10421.39 seconds total)