Starting phenix.real_space_refine on Thu May 22 10:50:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8y_42029/05_2025/8u8y_42029.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8y_42029/05_2025/8u8y_42029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8y_42029/05_2025/8u8y_42029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8y_42029/05_2025/8u8y_42029.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8y_42029/05_2025/8u8y_42029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8y_42029/05_2025/8u8y_42029.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 13.26, per 1000 atoms: 0.59 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: 5.04 Conformation dependent library (CDL) restraints added in 2.9 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: 3.05 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: 7.93 Time building geometry restraints manager: 5.96 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 - 1.58: 29677 1.58 - 3.17: 1164 3.17 - 4.75: 255 4.75 - 6.34: 32 6.34 - 7.92: 8 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=" N GLN F 265 " pdb=" CA GLN F 265 " pdb=" C GLN F 265 " ideal model delta sigma weight residual 111.82 108.39 3.43 1.16e+00 7.43e-01 8.74e+00 angle pdb=" N GLN C 265 " pdb=" CA GLN C 265 " pdb=" C GLN C 265 " ideal model delta sigma weight residual 111.82 108.46 3.36 1.16e+00 7.43e-01 8.40e+00 angle pdb=" O1P IMP C 601 " pdb=" P IMP C 601 " pdb=" O2P IMP C 601 " ideal model delta sigma weight residual 109.50 117.42 -7.92 3.00e+00 1.11e-01 6.97e+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 - 0.032: 2031 0.032 - 0.064: 988 0.064 - 0.096: 311 0.096 - 0.129: 167 0.129 - 0.161: 63 Chirality restraints: 3560 Sorted by residual: chirality pdb=" CA ILE G 447 " pdb=" N ILE G 447 " pdb=" C ILE G 447 " pdb=" CB ILE G 447 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE D 447 " pdb=" N ILE D 447 " pdb=" C ILE D 447 " pdb=" CB ILE D 447 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA ILE B 447 " pdb=" N ILE B 447 " pdb=" C ILE B 447 " pdb=" CB ILE B 447 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 3557 not shown) Planarity restraints: 3936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 457 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO H 458 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 458 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 458 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 457 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO G 458 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 458 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 458 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 457 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO A 458 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.024 5.00e-02 4.00e+02 ... (remaining 3933 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 7023 2.84 - 3.36: 21145 3.36 - 3.87: 39378 3.87 - 4.39: 47738 4.39 - 4.90: 75403 Nonbonded interactions: 190687 Sorted by model distance: nonbonded pdb=" OE1 GLN A 283 " pdb=" N GLY A 302 " model vdw 2.328 3.120 nonbonded pdb=" OE1 GLN C 283 " pdb=" N GLY C 302 " model vdw 2.329 3.120 nonbonded pdb=" OE1 GLN E 283 " pdb=" N GLY E 302 " model vdw 2.329 3.120 nonbonded pdb=" OE1 GLN B 283 " pdb=" N GLY B 302 " model vdw 2.329 3.120 nonbonded pdb=" OE1 GLN H 283 " pdb=" N GLY H 302 " model vdw 2.330 3.120 ... (remaining 190682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 49.150 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.144 23008 Z= 0.332 Angle : 0.754 7.922 31136 Z= 0.399 Chirality : 0.047 0.161 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (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 HIS 0.004 0.001 HIS H 466 PHE 0.014 0.002 PHE E 357 TYR 0.010 0.002 TYR B 353 ARG 0.003 0.001 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.14401 ( 944) hydrogen bonds : angle 5.86844 ( 2640) covalent geometry : bond 0.00664 (23008) covalent geometry : angle 0.75365 (31136) *********************** 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 : 2.254 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: 0.8051 (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: 1.7125 time to fit residues: 706.9006 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 : 2.290 ------------------------------------------------------------------------------- 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 243 optimal weight: 0.0000 chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.0470 chunk 225 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 112 GLN 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 = 0.3776 r_free = 0.3776 target = 0.160957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134731 restraints weight = 15713.413| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 0.88 r_work: 0.3372 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 23008 Z= 0.090 Angle : 0.455 3.856 31136 Z= 0.249 Chirality : 0.040 0.127 3560 Planarity : 0.003 0.034 3936 Dihedral : 10.283 84.310 3728 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.05 % Allowed : 13.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.16), residues: 2888 helix: 1.99 (0.15), residues: 1224 sheet: 0.32 (0.39), residues: 216 loop : -0.24 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 92 PHE 0.006 0.001 PHE B 99 TYR 0.006 0.001 TYR A 353 ARG 0.001 0.000 ARG H 57 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 944) hydrogen bonds : angle 4.97293 ( 2640) covalent geometry : bond 0.00179 (23008) covalent geometry : angle 0.45480 (31136) *********************** 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 421 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 373 time to evaluate : 2.356 Fit side-chains REVERT: A 111 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6516 (mm-30) REVERT: B 111 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6521 (mm-30) REVERT: D 444 SER cc_start: 0.8817 (t) cc_final: 0.8545 (m) REVERT: E 111 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6507 (mm-30) REVERT: F 444 SER cc_start: 0.8817 (t) cc_final: 0.8543 (m) REVERT: H 111 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6510 (mm-30) outliers start: 48 outliers final: 13 residues processed: 408 average time/residue: 1.6061 time to fit residues: 734.8255 Evaluate side-chains 358 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 341 time to evaluate : 2.392 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 455 LYS 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 260 LEU Chi-restraints excluded: chain F residue 455 LYS 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 63 optimal weight: 8.9990 chunk 103 optimal weight: 0.0050 chunk 107 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 176 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN C 94 ASN D 94 ASN D 292 GLN E 94 ASN E 292 GLN F 94 ASN F 265 GLN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129296 restraints weight = 15305.774| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 0.89 r_work: 0.3304 rms_B_bonded: 1.24 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: 0.8562 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23008 Z= 0.126 Angle : 0.529 4.760 31136 Z= 0.289 Chirality : 0.043 0.131 3560 Planarity : 0.004 0.036 3936 Dihedral : 9.167 99.471 3660 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.61 % Allowed : 12.93 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 2888 helix: 2.01 (0.15), residues: 1224 sheet: 0.04 (0.35), residues: 232 loop : -0.23 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 466 PHE 0.010 0.001 PHE H 490 TYR 0.007 0.001 TYR B 353 ARG 0.001 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 944) hydrogen bonds : angle 4.92158 ( 2640) covalent geometry : bond 0.00245 (23008) covalent geometry : angle 0.52883 (31136) *********************** 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 417 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 356 time to evaluate : 2.496 Fit side-chains REVERT: C 111 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: D 111 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6560 (mm-30) REVERT: E 111 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6506 (mm-30) REVERT: F 111 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6543 (mm-30) REVERT: G 111 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6563 (mm-30) outliers start: 61 outliers final: 43 residues processed: 399 average time/residue: 1.5855 time to fit residues: 706.7319 Evaluate side-chains 403 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 355 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP 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 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 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 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 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 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 111 GLU 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 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 242 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 74 optimal weight: 0.0980 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN D 94 ASN D 265 GLN D 292 GLN E 94 ASN E 265 GLN E 292 GLN F 94 ASN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127164 restraints weight = 15487.846| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 0.89 r_work: 0.3273 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23008 Z= 0.161 Angle : 0.603 5.554 31136 Z= 0.328 Chirality : 0.046 0.136 3560 Planarity : 0.004 0.038 3936 Dihedral : 9.140 108.400 3651 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.95 % Allowed : 12.50 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 2888 helix: 1.93 (0.15), residues: 1224 sheet: -0.03 (0.33), residues: 248 loop : -0.29 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 466 PHE 0.011 0.002 PHE C 99 TYR 0.009 0.002 TYR H 353 ARG 0.002 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.05897 ( 944) hydrogen bonds : angle 5.03709 ( 2640) covalent geometry : bond 0.00320 (23008) covalent geometry : angle 0.60280 (31136) *********************** 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 428 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 359 time to evaluate : 2.485 Fit side-chains REVERT: A 111 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6677 (mm-30) REVERT: B 111 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: C 111 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6703 (mm-30) REVERT: D 111 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: E 111 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6666 (mm-30) REVERT: F 111 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: G 111 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: H 111 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6685 (mm-30) outliers start: 69 outliers final: 53 residues processed: 407 average time/residue: 1.6259 time to fit residues: 738.2550 Evaluate side-chains 414 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 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 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 455 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 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 277 GLN 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 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 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 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 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 14 optimal weight: 3.9990 chunk 277 optimal weight: 7.9990 chunk 103 optimal weight: 0.0020 chunk 193 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 149 optimal weight: 0.0060 chunk 253 optimal weight: 0.3980 chunk 111 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.6806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN C 265 GLN D 94 ASN E 94 ASN F 94 ASN F 265 GLN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.158829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.132420 restraints weight = 15625.925| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 0.88 r_work: 0.3344 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1091 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= 0.096 Angle : 0.465 4.376 31136 Z= 0.254 Chirality : 0.041 0.125 3560 Planarity : 0.003 0.035 3936 Dihedral : 8.326 91.177 3651 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.65 % Allowed : 12.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.16), residues: 2888 helix: 2.20 (0.15), residues: 1224 sheet: 0.54 (0.33), residues: 272 loop : -0.26 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 466 PHE 0.008 0.001 PHE F 490 TYR 0.007 0.001 TYR A 353 ARG 0.001 0.000 ARG E 259 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 944) hydrogen bonds : angle 4.72100 ( 2640) covalent geometry : bond 0.00186 (23008) covalent geometry : angle 0.46491 (31136) *********************** 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 435 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 373 time to evaluate : 2.392 Fit side-chains REVERT: A 111 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6485 (mm-30) REVERT: B 111 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6503 (mm-30) REVERT: C 111 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6502 (mm-30) REVERT: D 111 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6516 (mm-30) REVERT: E 111 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6478 (mm-30) REVERT: F 111 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6513 (mm-30) REVERT: G 111 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6501 (mm-30) REVERT: H 111 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6502 (mm-30) REVERT: H 444 SER cc_start: 0.8708 (t) cc_final: 0.8507 (m) outliers start: 62 outliers final: 25 residues processed: 419 average time/residue: 1.5720 time to fit residues: 736.4978 Evaluate side-chains 396 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 363 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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 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 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 455 LYS 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 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 330 ILE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 16 ASP 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 111 GLU Chi-restraints excluded: chain H residue 330 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 224 optimal weight: 3.9990 chunk 281 optimal weight: 9.9990 chunk 144 optimal weight: 0.0470 chunk 280 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 266 optimal weight: 7.9990 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN D 94 ASN D 292 GLN E 94 ASN E 265 GLN E 292 GLN F 94 ASN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127796 restraints weight = 15396.712| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 0.88 r_work: 0.3282 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23008 Z= 0.152 Angle : 0.579 5.456 31136 Z= 0.315 Chirality : 0.045 0.136 3560 Planarity : 0.004 0.037 3936 Dihedral : 8.913 107.469 3651 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.65 % Allowed : 12.84 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 2888 helix: 2.02 (0.15), residues: 1224 sheet: 0.04 (0.32), residues: 248 loop : -0.32 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 466 PHE 0.010 0.002 PHE F 99 TYR 0.009 0.002 TYR C 353 ARG 0.002 0.000 ARG H 355 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 944) hydrogen bonds : angle 4.92319 ( 2640) covalent geometry : bond 0.00301 (23008) covalent geometry : angle 0.57915 (31136) *********************** 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 426 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 2.306 Fit side-chains REVERT: A 111 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6618 (mm-30) REVERT: B 111 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6639 (mm-30) REVERT: C 111 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: D 111 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6657 (mm-30) REVERT: E 111 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: F 111 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6657 (mm-30) REVERT: G 111 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6654 (mm-30) REVERT: H 111 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6624 (mm-30) outliers start: 62 outliers final: 38 residues processed: 414 average time/residue: 1.6368 time to fit residues: 756.4756 Evaluate side-chains 397 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 2.534 ------------------------------------------------------------------------------- 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 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 111 GLU 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 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 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 111 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 203 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 0.0170 chunk 216 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 228 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.158300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131914 restraints weight = 15598.018| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.88 r_work: 0.3338 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1164 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= 0.098 Angle : 0.470 4.477 31136 Z= 0.256 Chirality : 0.041 0.125 3560 Planarity : 0.003 0.035 3936 Dihedral : 8.289 92.742 3651 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.05 % Allowed : 13.27 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2888 helix: 2.20 (0.15), residues: 1224 sheet: 0.47 (0.32), residues: 272 loop : -0.27 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 466 PHE 0.008 0.001 PHE G 490 TYR 0.006 0.001 TYR A 353 ARG 0.001 0.000 ARG G 57 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 944) hydrogen bonds : angle 4.68767 ( 2640) covalent geometry : bond 0.00189 (23008) covalent geometry : angle 0.46981 (31136) *********************** 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 407 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 2.421 Fit side-chains REVERT: A 111 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6522 (mm-30) REVERT: B 111 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6519 (mm-30) REVERT: C 111 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6496 (mm-30) REVERT: D 111 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6516 (mm-30) REVERT: E 111 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6616 (mm-30) REVERT: F 111 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6529 (mm-30) REVERT: G 111 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6514 (mm-30) REVERT: H 111 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6535 (mm-30) outliers start: 48 outliers final: 31 residues processed: 399 average time/residue: 1.6924 time to fit residues: 751.8984 Evaluate side-chains 393 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 354 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 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 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 111 GLU 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 111 GLU Chi-restraints excluded: chain D residue 261 ASP 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 111 GLU 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 16 ASP Chi-restraints excluded: chain G residue 63 THR 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 111 GLU Chi-restraints excluded: chain H residue 330 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 24 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN C 94 ASN C 265 GLN D 94 ASN D 265 GLN E 94 ASN E 265 GLN F 94 ASN F 265 GLN G 94 ASN H 94 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.124318 restraints weight = 15369.892| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.88 r_work: 0.3237 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23008 Z= 0.266 Angle : 0.782 7.031 31136 Z= 0.423 Chirality : 0.054 0.164 3560 Planarity : 0.006 0.052 3936 Dihedral : 9.422 109.626 3651 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.23 % Allowed : 14.04 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 2888 helix: 1.71 (0.15), residues: 1224 sheet: 0.14 (0.32), residues: 248 loop : -0.32 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 466 PHE 0.016 0.003 PHE A 357 TYR 0.013 0.003 TYR F 353 ARG 0.004 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.07567 ( 944) hydrogen bonds : angle 5.22397 ( 2640) covalent geometry : bond 0.00549 (23008) covalent geometry : angle 0.78250 (31136) *********************** 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 415 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 363 time to evaluate : 2.322 Fit side-chains REVERT: A 111 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: B 111 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6836 (mm-30) REVERT: E 111 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: H 111 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6842 (mm-30) outliers start: 52 outliers final: 36 residues processed: 405 average time/residue: 1.5926 time to fit residues: 721.7805 Evaluate side-chains 386 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 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 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 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 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 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 221 optimal weight: 6.9990 chunk 1 optimal weight: 0.0060 chunk 180 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 246 optimal weight: 0.0670 chunk 143 optimal weight: 0.0000 chunk 94 optimal weight: 3.9990 overall best weight: 0.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.159823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133739 restraints weight = 15676.010| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.88 r_work: 0.3364 rms_B_bonded: 1.23 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: 0.8503 moved from start: 0.1279 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= 0.090 Angle : 0.454 4.099 31136 Z= 0.248 Chirality : 0.040 0.124 3560 Planarity : 0.003 0.035 3936 Dihedral : 8.215 86.560 3651 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.24 % Allowed : 14.47 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.16), residues: 2888 helix: 2.14 (0.15), residues: 1224 sheet: 0.51 (0.32), residues: 272 loop : -0.18 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 92 PHE 0.007 0.001 PHE G 490 TYR 0.006 0.001 TYR F 353 ARG 0.001 0.000 ARG G 105 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 944) hydrogen bonds : angle 4.68872 ( 2640) covalent geometry : bond 0.00174 (23008) covalent geometry : angle 0.45442 (31136) *********************** 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 384 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 355 time to evaluate : 2.364 Fit side-chains REVERT: A 111 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: C 111 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6524 (mm-30) REVERT: D 111 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: F 111 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6540 (mm-30) REVERT: G 111 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: H 111 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6528 (mm-30) outliers start: 29 outliers final: 14 residues processed: 384 average time/residue: 1.6312 time to fit residues: 698.5292 Evaluate side-chains 370 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 350 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 B residue 261 ASP 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 330 ILE Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 7.9990 chunk 266 optimal weight: 7.9990 chunk 273 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 252 optimal weight: 0.0000 chunk 146 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 0.0000 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN C 94 ASN C 265 GLN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.158495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132119 restraints weight = 15673.362| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 0.89 r_work: 0.3339 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1220 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= 0.100 Angle : 0.477 4.450 31136 Z= 0.259 Chirality : 0.041 0.128 3560 Planarity : 0.003 0.035 3936 Dihedral : 8.134 88.927 3648 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.86 % Allowed : 15.54 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.15), residues: 2888 helix: 2.17 (0.15), residues: 1224 sheet: 0.52 (0.32), residues: 272 loop : -0.19 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 92 PHE 0.009 0.001 PHE A 490 TYR 0.006 0.001 TYR F 353 ARG 0.002 0.000 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 944) hydrogen bonds : angle 4.66227 ( 2640) covalent geometry : bond 0.00196 (23008) covalent geometry : angle 0.47728 (31136) ********************** 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 369 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 349 time to evaluate : 2.398 Fit side-chains REVERT: A 111 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6536 (mm-30) REVERT: B 111 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: C 111 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: D 111 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6541 (mm-30) REVERT: F 111 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: G 111 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6533 (mm-30) REVERT: H 111 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6500 (mm-30) outliers start: 20 outliers final: 15 residues processed: 367 average time/residue: 1.6826 time to fit residues: 689.5743 Evaluate side-chains 374 residues out of total 2336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 352 time to evaluate : 2.248 ------------------------------------------------------------------------------- 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 B residue 111 GLU 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 261 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 261 ASP Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 330 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 160 optimal weight: 4.9990 chunk 287 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 32 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125425 restraints weight = 15276.378| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 0.88 r_work: 0.3250 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23008 Z= 0.224 Angle : 0.717 6.656 31136 Z= 0.388 Chirality : 0.051 0.163 3560 Planarity : 0.005 0.048 3936 Dihedral : 9.123 112.539 3648 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.41 % Allowed : 14.73 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 2888 helix: 1.79 (0.15), residues: 1224 sheet: 0.14 (0.32), residues: 248 loop : -0.27 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 466 PHE 0.014 0.003 PHE A 357 TYR 0.011 0.002 TYR B 353 ARG 0.004 0.001 ARG F 407 Details of bonding type rmsd hydrogen bonds : bond 0.06885 ( 944) hydrogen bonds : angle 5.04239 ( 2640) covalent geometry : bond 0.00451 (23008) covalent geometry : angle 0.71656 (31136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20214.11 seconds wall clock time: 348 minutes 11.30 seconds (20891.30 seconds total)