Starting phenix.real_space_refine on Tue Jul 23 14:27:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/07_2024/8u8y_42029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/07_2024/8u8y_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/07_2024/8u8y_42029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/07_2024/8u8y_42029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/07_2024/8u8y_42029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/07_2024/8u8y_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 Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A ASP 239": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ASP 232": "OD1" <-> "OD2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E ASP 255": "OD1" <-> "OD2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 449": "OD1" <-> "OD2" Residue "E TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 28": "OD1" <-> "OD2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F ASP 255": "OD1" <-> "OD2" Residue "F TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 418": "OD1" <-> "OD2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G ASP 77": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G ASP 239": "OD1" <-> "OD2" Residue "G TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 449": "OD1" <-> "OD2" Residue "G TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 75": "OE1" <-> "OE2" Residue "H ASP 77": "OD1" <-> "OD2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H ASP 232": "OD1" <-> "OD2" Residue "H ASP 239": "OD1" <-> "OD2" Residue "H ASP 255": "OD1" <-> "OD2" Residue "H TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 261": "OD1" <-> "OD2" Residue "H GLU 335": "OE1" <-> "OE2" Residue "H PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 449": "OD1" <-> "OD2" Residue "H TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 12.68, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 9.38 Conformation dependent library (CDL) restraints added in 4.3 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: 3.01 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: 8.70 Time building geometry restraints manager: 10.08 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: 98.65 - 105.52: 440 105.52 - 112.40: 11480 112.40 - 119.28: 7542 119.28 - 126.15: 11442 126.15 - 133.03: 232 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 2.520 nonbonded pdb=" OE1 GLN C 283 " pdb=" N GLY C 302 " model vdw 2.329 2.520 nonbonded pdb=" OE1 GLN E 283 " pdb=" N GLY E 302 " model vdw 2.329 2.520 nonbonded pdb=" OE1 GLN B 283 " pdb=" N GLY B 302 " model vdw 2.329 2.520 nonbonded pdb=" OE1 GLN H 283 " pdb=" N GLY H 302 " model vdw 2.330 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 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: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 63.100 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.130 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:13.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.410 ------------------------------------------------------------------------------- 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= 0.439 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 *********************** 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 fitting. rotamer outliers: 41 poor density : 338 time to evaluate : 2.635 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: 1.7251 time to fit residues: 711.4484 Evaluate side-chains 368 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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: 9.9990 chunk 218 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 147 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 225 optimal weight: 0.0270 chunk 87 optimal weight: 0.1980 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 0.4980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 112 GLN B 94 ASN C 94 ASN C 265 GLN D 94 ASN D 112 GLN E 94 ASN F 94 ASN F 112 GLN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 94 ASN H 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.0947 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= 0.115 Angle : 0.445 3.991 31136 Z= 0.245 Chirality : 0.040 0.126 3560 Planarity : 0.003 0.034 3936 Dihedral : 10.278 84.684 3728 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 13.48 % Favored : 84.33 % 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: 1.98 (0.15), residues: 1224 sheet: 0.03 (0.36), residues: 232 loop : -0.17 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 92 PHE 0.006 0.001 PHE F 99 TYR 0.007 0.001 TYR B 353 ARG 0.002 0.000 ARG H 57 *********************** 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 417 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 366 time to evaluate : 2.431 Fit side-chains REVERT: A 111 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6510 (mm-30) REVERT: B 111 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6516 (mm-30) REVERT: C 111 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6503 (mm-30) REVERT: E 111 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: H 111 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6506 (mm-30) outliers start: 51 outliers final: 18 residues processed: 402 average time/residue: 1.5675 time to fit residues: 704.3113 Evaluate side-chains 368 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 345 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 277 GLN 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 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 277 GLN 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 277 GLN Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 277 GLN 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 145 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 217 optimal weight: 8.9990 chunk 178 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 283 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN B 292 GLN C 94 ASN D 94 ASN D 292 GLN E 94 ASN E 292 GLN F 94 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.0606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23008 Z= 0.262 Angle : 0.665 6.086 31136 Z= 0.361 Chirality : 0.049 0.142 3560 Planarity : 0.005 0.046 3936 Dihedral : 10.130 109.847 3678 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.91 % Allowed : 13.18 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.15), residues: 2888 helix: 1.76 (0.15), residues: 1224 sheet: -0.05 (0.34), residues: 248 loop : -0.28 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 466 PHE 0.013 0.002 PHE A 357 TYR 0.010 0.002 TYR B 353 ARG 0.002 0.001 ARG A 355 *********************** 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 414 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 346 time to evaluate : 2.562 Fit side-chains REVERT: B 111 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6777 (mm-30) outliers start: 68 outliers final: 58 residues processed: 392 average time/residue: 1.6316 time to fit residues: 711.9466 Evaluate side-chains 397 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 338 time to evaluate : 2.679 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 175 optimal weight: 0.0980 chunk 262 optimal weight: 9.9990 chunk 278 optimal weight: 0.4980 chunk 137 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 292 GLN C 94 ASN C 265 GLN D 94 ASN D 265 GLN D 292 GLN E 94 ASN E 265 GLN F 94 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 94 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23008 Z= 0.188 Angle : 0.569 5.536 31136 Z= 0.311 Chirality : 0.044 0.132 3560 Planarity : 0.004 0.038 3936 Dihedral : 9.884 107.932 3678 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.04 % Allowed : 12.20 % 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: 0.95 (0.15), residues: 2888 helix: 1.86 (0.15), residues: 1224 sheet: 0.02 (0.33), residues: 248 loop : -0.31 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 466 PHE 0.010 0.002 PHE C 99 TYR 0.008 0.001 TYR B 353 ARG 0.001 0.000 ARG C 57 *********************** 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 419 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 348 time to evaluate : 2.875 Fit side-chains REVERT: A 111 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6736 (mm-30) REVERT: B 111 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6745 (mm-30) REVERT: C 111 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: C 265 GLN cc_start: 0.8015 (mt0) cc_final: 0.7768 (mt0) REVERT: D 111 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6732 (mm-30) REVERT: E 111 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6679 (mm-30) REVERT: F 111 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: G 111 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6711 (mm-30) REVERT: H 111 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6733 (mm-30) outliers start: 71 outliers final: 50 residues processed: 397 average time/residue: 1.6358 time to fit residues: 723.3593 Evaluate side-chains 411 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 353 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 192 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 292 GLN C 94 ASN D 94 ASN D 265 GLN E 94 ASN E 265 GLN F 94 ASN F 265 GLN G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0732 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= 0.201 Angle : 0.592 5.807 31136 Z= 0.323 Chirality : 0.045 0.136 3560 Planarity : 0.004 0.038 3936 Dihedral : 9.886 108.061 3678 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.25 % Allowed : 12.41 % Favored : 84.33 % 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: 0.93 (0.15), residues: 2888 helix: 1.85 (0.15), residues: 1224 sheet: 0.04 (0.33), residues: 248 loop : -0.34 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 466 PHE 0.010 0.002 PHE F 99 TYR 0.008 0.002 TYR H 353 ARG 0.001 0.000 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 343 time to evaluate : 2.657 Fit side-chains REVERT: A 111 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: B 111 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6723 (mm-30) REVERT: C 111 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: C 265 GLN cc_start: 0.7982 (mt0) cc_final: 0.7774 (mt0) REVERT: D 111 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6768 (mm-30) REVERT: E 111 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6676 (mm-30) REVERT: F 111 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: G 111 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6752 (mm-30) REVERT: H 111 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6710 (mm-30) outliers start: 76 outliers final: 53 residues processed: 405 average time/residue: 1.6506 time to fit residues: 744.0522 Evaluate side-chains 398 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 337 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 146 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN B 292 GLN C 94 ASN D 94 ASN E 94 ASN F 94 ASN F 265 GLN G 94 ASN H 94 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23008 Z= 0.237 Angle : 0.644 6.374 31136 Z= 0.350 Chirality : 0.047 0.142 3560 Planarity : 0.005 0.040 3936 Dihedral : 10.009 108.479 3678 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.95 % Allowed : 13.18 % 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: 0.85 (0.15), residues: 2888 helix: 1.77 (0.15), residues: 1224 sheet: 0.07 (0.33), residues: 248 loop : -0.39 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 466 PHE 0.011 0.002 PHE G 99 TYR 0.009 0.002 TYR B 353 ARG 0.002 0.001 ARG G 322 *********************** 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 406 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 337 time to evaluate : 2.550 Fit side-chains REVERT: A 111 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6789 (mm-30) REVERT: B 111 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6803 (mm-30) REVERT: C 111 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6788 (mm-30) REVERT: E 111 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: H 111 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6787 (mm-30) outliers start: 69 outliers final: 61 residues processed: 390 average time/residue: 1.5934 time to fit residues: 693.0619 Evaluate side-chains 403 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 337 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 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 410 LYS 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 410 LYS Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 410 LYS Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 277 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 169 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23008 Z= 0.150 Angle : 0.519 5.236 31136 Z= 0.284 Chirality : 0.042 0.130 3560 Planarity : 0.004 0.038 3936 Dihedral : 9.575 101.540 3678 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.91 % Allowed : 13.48 % 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: 1.11 (0.15), residues: 2888 helix: 1.98 (0.15), residues: 1224 sheet: 0.43 (0.31), residues: 288 loop : -0.32 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 466 PHE 0.008 0.001 PHE B 490 TYR 0.007 0.001 TYR E 353 ARG 0.002 0.000 ARG B 57 *********************** 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 425 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 357 time to evaluate : 2.481 Fit side-chains REVERT: A 111 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6624 (mm-30) REVERT: B 111 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6657 (mm-30) REVERT: C 111 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6613 (mm-30) REVERT: D 111 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6638 (mm-30) REVERT: E 111 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: F 111 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6595 (mm-30) REVERT: G 111 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6621 (mm-30) REVERT: H 111 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6622 (mm-30) outliers start: 68 outliers final: 46 residues processed: 412 average time/residue: 1.5947 time to fit residues: 733.0388 Evaluate side-chains 403 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 349 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 189 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 292 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1072 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= 0.130 Angle : 0.479 4.667 31136 Z= 0.261 Chirality : 0.041 0.129 3560 Planarity : 0.003 0.037 3936 Dihedral : 8.831 91.953 3666 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.35 % Allowed : 14.60 % Favored : 83.05 % 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: 1.27 (0.16), residues: 2888 helix: 2.12 (0.15), residues: 1224 sheet: 0.65 (0.33), residues: 272 loop : -0.25 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 92 PHE 0.007 0.001 PHE B 490 TYR 0.006 0.001 TYR C 353 ARG 0.001 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 361 time to evaluate : 2.787 Fit side-chains REVERT: D 111 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6603 (mm-30) REVERT: F 111 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: G 111 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6577 (mm-30) outliers start: 55 outliers final: 33 residues processed: 403 average time/residue: 1.5744 time to fit residues: 709.5514 Evaluate side-chains 384 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 348 time to evaluate : 2.282 ------------------------------------------------------------------------------- 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 330 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 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 277 GLN Chi-restraints excluded: chain C residue 330 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 455 LYS Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 330 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 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 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.0050 chunk 265 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 257 optimal weight: 7.9990 overall best weight: 3.1600 ------------------------------------------------------------------------------- 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 ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN ** F 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 94 ASN H 292 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23008 Z= 0.283 Angle : 0.693 6.586 31136 Z= 0.376 Chirality : 0.049 0.153 3560 Planarity : 0.005 0.041 3936 Dihedral : 9.294 110.870 3651 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.67 % Allowed : 15.03 % Favored : 83.30 % 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: 0.91 (0.15), residues: 2888 helix: 1.83 (0.15), residues: 1224 sheet: 0.11 (0.32), residues: 248 loop : -0.38 (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 H 357 TYR 0.011 0.002 TYR E 353 ARG 0.003 0.001 ARG B 322 *********************** 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 387 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 348 time to evaluate : 2.447 Fit side-chains outliers start: 39 outliers final: 39 residues processed: 379 average time/residue: 1.6736 time to fit residues: 705.5963 Evaluate side-chains 377 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 338 time to evaluate : 2.737 ------------------------------------------------------------------------------- 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 330 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 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 277 GLN Chi-restraints excluded: chain C residue 330 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 277 GLN Chi-restraints excluded: chain D residue 330 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 277 GLN Chi-restraints excluded: chain E residue 330 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 277 GLN 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 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 286 optimal weight: 0.5980 chunk 264 optimal weight: 8.9990 chunk 228 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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 G 94 ASN G 292 GLN H 94 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0843 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= 0.222 Angle : 0.617 5.849 31136 Z= 0.336 Chirality : 0.046 0.145 3560 Planarity : 0.004 0.038 3936 Dihedral : 9.151 108.130 3651 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.67 % Allowed : 14.64 % Favored : 83.69 % 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: 0.96 (0.15), residues: 2888 helix: 1.83 (0.15), residues: 1224 sheet: 0.46 (0.31), residues: 288 loop : -0.39 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 466 PHE 0.011 0.002 PHE G 99 TYR 0.009 0.002 TYR G 353 ARG 0.002 0.000 ARG D 322 ********************** 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 375 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 336 time to evaluate : 2.627 Fit side-chains outliers start: 39 outliers final: 36 residues processed: 367 average time/residue: 1.6955 time to fit residues: 694.5856 Evaluate side-chains 373 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 337 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 330 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 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 277 GLN Chi-restraints excluded: chain C residue 330 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 455 LYS Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 330 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 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 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 7.9990 chunk 243 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 210 optimal weight: 20.0000 chunk 33 optimal weight: 0.0970 chunk 63 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- 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 G 94 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126150 restraints weight = 15256.038| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 0.88 r_work: 0.3262 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23008 Z= 0.231 Angle : 0.637 6.182 31136 Z= 0.346 Chirality : 0.047 0.148 3560 Planarity : 0.004 0.039 3936 Dihedral : 9.178 108.383 3651 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.76 % Allowed : 14.64 % 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: 0.94 (0.15), residues: 2888 helix: 1.79 (0.15), residues: 1224 sheet: 0.46 (0.31), residues: 288 loop : -0.37 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 466 PHE 0.011 0.002 PHE B 99 TYR 0.009 0.002 TYR A 353 ARG 0.002 0.000 ARG G 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10581.69 seconds wall clock time: 184 minutes 47.93 seconds (11087.93 seconds total)