Starting phenix.real_space_refine on Tue Mar 19 00:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/03_2024/8u8y_42029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/03_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_42029/03_2024/8u8y_42029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/03_2024/8u8y_42029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/03_2024/8u8y_42029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u8y_42029/03_2024/8u8y_42029_updated.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 11.53, per 1000 atoms: 0.51 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: 8.94 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... running ksdssp... Secondary structure from input PDB file: 120 helices and 32 sheets defined 37.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 48.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 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 333 through 337 Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.301A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 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 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.294A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 254 through 266 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 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 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.293A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 254 through 266 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 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 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.291A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 420 No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 254 through 266 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 316 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 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.292A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 254 through 266 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 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 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.295A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 417 through 420 No H-bonds generated for 'chain 'F' and resid 417 through 420' Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 254 through 266 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 316 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 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.294A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 417 through 420 No H-bonds generated for 'chain 'G' and resid 417 through 420' Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 254 through 266 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 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 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.297A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 420 No H-bonds generated for 'chain 'H' and resid 417 through 420' Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.493A pdb=" N VAL A 384 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 383 " --> pdb=" O ILE A 361 " (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) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.557A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 272 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A 298 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.493A pdb=" N VAL B 384 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 383 " --> pdb=" O ILE B 361 " (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) Processing sheet with id= G, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.558A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL B 272 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN B 298 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.493A pdb=" N VAL C 384 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 383 " --> pdb=" O ILE C 361 " (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) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.559A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL C 272 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN C 298 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.484A pdb=" N VAL D 384 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 383 " --> pdb=" O ILE D 361 " (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) Processing sheet with id= O, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.560A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 272 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN D 298 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 401 through 403 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.493A pdb=" N VAL E 384 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 383 " --> pdb=" O ILE E 361 " (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) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.557A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL E 272 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN E 298 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= U, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.493A pdb=" N VAL F 384 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 383 " --> pdb=" O ILE F 361 " (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) Processing sheet with id= W, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.559A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL F 272 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN F 298 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= Y, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.493A pdb=" N VAL G 384 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR G 383 " --> pdb=" O ILE G 361 " (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) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.559A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL G 272 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 298 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AC, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.491A pdb=" N VAL H 384 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR H 383 " --> pdb=" O ILE H 361 " (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) Processing sheet with id= AE, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.557A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL H 272 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN H 298 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 401 through 403 680 hydrogen bonds defined for protein. 1752 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: 6.41 Time building geometry restraints manager: 9.74 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=" N THR D 74 " pdb=" CA THR D 74 " pdb=" C THR D 74 " ideal model delta sigma weight residual 108.02 112.44 -4.42 1.75e+00 3.27e-01 6.38e+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: 7063 2.84 - 3.36: 21366 3.36 - 3.87: 39697 3.87 - 4.39: 48158 4.39 - 4.90: 75459 Nonbonded interactions: 191743 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 191738 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.450 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 59.740 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.210 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.580 ------------------------------------------------------------------------------- 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= 0.428 Angle : 0.743 5.338 31136 Z= 0.397 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 : 2.648 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: 1.7225 time to fit residues: 709.2176 Evaluate side-chains 368 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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: 6.9990 chunk 74 optimal weight: 0.1980 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 G 94 ASN H 94 ASN H 112 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 23008 Z= 0.133 Angle : 0.478 4.724 31136 Z= 0.260 Chirality : 0.042 0.142 3560 Planarity : 0.004 0.036 3936 Dihedral : 10.539 96.321 3728 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.53 % Allowed : 13.01 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2888 helix: 1.54 (0.15), residues: 1224 sheet: 0.02 (0.35), residues: 232 loop : -0.25 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 466 PHE 0.007 0.001 PHE B 490 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 431 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 372 time to evaluate : 2.608 Fit side-chains REVERT: A 111 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: B 111 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6737 (mm-30) REVERT: C 111 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: D 111 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: E 111 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: F 111 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6709 (mm-30) REVERT: G 111 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: H 111 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6714 (mm-30) outliers start: 59 outliers final: 37 residues processed: 418 average time/residue: 1.5600 time to fit residues: 730.2568 Evaluate side-chains 393 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 348 time to evaluate : 2.773 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 361 ILE 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: 6.9990 chunk 217 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN D 94 ASN D 265 GLN D 292 GLN E 94 ASN E 265 GLN E 292 GLN F 94 ASN F 292 GLN G 94 ASN G 292 GLN H 94 ASN H 292 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0577 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= 0.253 Angle : 0.647 6.288 31136 Z= 0.349 Chirality : 0.048 0.142 3560 Planarity : 0.005 0.044 3936 Dihedral : 10.859 113.463 3709 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.61 % Allowed : 13.44 % 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: 0.54 (0.15), residues: 2888 helix: 1.25 (0.15), residues: 1224 sheet: -0.06 (0.32), residues: 248 loop : -0.29 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 466 PHE 0.013 0.002 PHE F 99 TYR 0.010 0.002 TYR B 353 ARG 0.002 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 356 time to evaluate : 2.685 Fit side-chains outliers start: 61 outliers final: 61 residues processed: 404 average time/residue: 1.6224 time to fit residues: 729.5173 Evaluate side-chains 414 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 353 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 chunk 125 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 262 optimal weight: 9.9990 chunk 278 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN D 94 ASN D 292 GLN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23008 Z= 0.135 Angle : 0.482 5.073 31136 Z= 0.261 Chirality : 0.042 0.141 3560 Planarity : 0.004 0.037 3936 Dihedral : 10.181 98.171 3709 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.95 % Allowed : 13.44 % 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: 0.77 (0.15), residues: 2888 helix: 1.42 (0.15), residues: 1224 sheet: 0.33 (0.35), residues: 232 loop : -0.19 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 466 PHE 0.008 0.001 PHE D 490 TYR 0.007 0.001 TYR A 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 454 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 385 time to evaluate : 2.795 Fit side-chains REVERT: A 111 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6712 (mm-30) REVERT: B 111 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6737 (mm-30) REVERT: C 111 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: D 111 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6734 (mm-30) REVERT: E 111 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: F 111 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6723 (mm-30) REVERT: G 111 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: H 111 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6711 (mm-30) outliers start: 69 outliers final: 50 residues processed: 431 average time/residue: 1.5623 time to fit residues: 752.4896 Evaluate side-chains 416 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 358 time to evaluate : 2.543 ------------------------------------------------------------------------------- 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 260 LEU 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 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 47 ASP Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.8497 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23008 Z= 0.237 Angle : 0.627 6.309 31136 Z= 0.338 Chirality : 0.047 0.141 3560 Planarity : 0.005 0.042 3936 Dihedral : 10.416 112.667 3697 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.42 % Allowed : 12.67 % 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: 0.56 (0.15), residues: 2888 helix: 1.25 (0.15), residues: 1224 sheet: 0.15 (0.33), residues: 248 loop : -0.30 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 466 PHE 0.013 0.002 PHE B 99 TYR 0.010 0.002 TYR A 353 ARG 0.002 0.001 ARG F 341 *********************** 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 448 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 368 time to evaluate : 2.596 Fit side-chains REVERT: A 111 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: B 111 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: C 111 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6817 (mm-30) REVERT: D 111 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: E 111 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6823 (mm-30) REVERT: F 111 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6814 (mm-30) REVERT: G 111 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6814 (mm-30) REVERT: H 111 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6813 (mm-30) outliers start: 80 outliers final: 56 residues processed: 424 average time/residue: 1.6253 time to fit residues: 767.9222 Evaluate side-chains 420 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 356 time to evaluate : 2.574 ------------------------------------------------------------------------------- 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 260 LEU 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 260 LEU 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 260 LEU 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: 5.9990 chunk 250 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 163 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23008 Z= 0.171 Angle : 0.535 5.486 31136 Z= 0.290 Chirality : 0.044 0.137 3560 Planarity : 0.004 0.038 3936 Dihedral : 10.116 105.446 3697 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.87 % Allowed : 13.44 % 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: 0.63 (0.15), residues: 2888 helix: 1.31 (0.15), residues: 1224 sheet: 0.25 (0.32), residues: 248 loop : -0.28 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 466 PHE 0.009 0.002 PHE B 99 TYR 0.008 0.001 TYR A 353 ARG 0.001 0.000 ARG H 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 424 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 357 time to evaluate : 2.583 Fit side-chains REVERT: A 111 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6762 (mm-30) REVERT: B 261 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6991 (t70) REVERT: C 111 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6750 (mm-30) REVERT: D 111 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6762 (mm-30) REVERT: D 261 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.7009 (t70) REVERT: E 111 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6772 (mm-30) REVERT: F 111 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6743 (mm-30) REVERT: G 111 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: H 111 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6759 (mm-30) outliers start: 67 outliers final: 51 residues processed: 405 average time/residue: 1.6387 time to fit residues: 742.3009 Evaluate side-chains 420 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 360 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 261 ASP 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 261 ASP 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 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 260 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 0.0170 chunk 155 optimal weight: 0.0570 chunk 277 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.7340 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23008 Z= 0.182 Angle : 0.556 5.691 31136 Z= 0.300 Chirality : 0.045 0.139 3560 Planarity : 0.004 0.038 3936 Dihedral : 10.037 106.000 3694 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.78 % Allowed : 14.08 % Favored : 83.13 % 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: 0.60 (0.15), residues: 2888 helix: 1.28 (0.15), residues: 1224 sheet: 0.20 (0.32), residues: 248 loop : -0.29 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 466 PHE 0.010 0.002 PHE H 99 TYR 0.008 0.001 TYR H 353 ARG 0.001 0.000 ARG G 322 *********************** 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 423 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 358 time to evaluate : 2.572 Fit side-chains REVERT: B 261 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.7036 (t70) REVERT: C 111 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6768 (mm-30) REVERT: F 111 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: G 111 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6774 (mm-30) outliers start: 65 outliers final: 53 residues processed: 405 average time/residue: 1.5854 time to fit residues: 717.0785 Evaluate side-chains 412 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 355 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 260 LEU 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 260 LEU Chi-restraints excluded: chain B residue 261 ASP 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 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 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 260 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 218 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 265 GLN C 94 ASN D 94 ASN E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0893 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= 0.154 Angle : 0.509 5.176 31136 Z= 0.275 Chirality : 0.043 0.139 3560 Planarity : 0.004 0.037 3936 Dihedral : 9.434 103.664 3682 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.48 % Allowed : 14.21 % 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: 0.70 (0.15), residues: 2888 helix: 1.36 (0.15), residues: 1224 sheet: 0.30 (0.32), residues: 248 loop : -0.23 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 466 PHE 0.008 0.001 PHE F 490 TYR 0.008 0.001 TYR G 353 ARG 0.001 0.000 ARG F 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 417 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 359 time to evaluate : 2.513 Fit side-chains REVERT: G 111 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6684 (mm-30) outliers start: 58 outliers final: 53 residues processed: 399 average time/residue: 1.5357 time to fit residues: 686.2654 Evaluate side-chains 409 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 355 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 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 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 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 63 THR 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 260 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 455 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 242 optimal weight: 0.0770 chunk 258 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 203 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN C 94 ASN D 94 ASN D 265 GLN D 292 GLN E 94 ASN F 94 ASN G 94 ASN G 292 GLN H 94 ASN H 292 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1057 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= 0.120 Angle : 0.450 4.375 31136 Z= 0.243 Chirality : 0.041 0.143 3560 Planarity : 0.003 0.036 3936 Dihedral : 8.766 92.345 3676 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.18 % Allowed : 14.55 % Favored : 83.26 % 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: 1.49 (0.15), residues: 1224 sheet: 0.49 (0.33), residues: 248 loop : -0.19 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 466 PHE 0.007 0.001 PHE F 490 TYR 0.006 0.001 TYR H 353 ARG 0.002 0.000 ARG F 57 *********************** 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 425 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 374 time to evaluate : 2.594 Fit side-chains outliers start: 51 outliers final: 45 residues processed: 408 average time/residue: 1.5578 time to fit residues: 711.1465 Evaluate side-chains 410 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 365 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 63 THR 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 455 LYS Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 63 THR 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 260 LEU 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 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 330 ILE Chi-restraints excluded: chain G residue 455 LYS Chi-restraints excluded: chain H residue 16 ASP Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 277 GLN 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: 8.9990 chunk 273 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 190 optimal weight: 0.0050 chunk 286 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 228 optimal weight: 0.2980 chunk 23 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0963 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= 0.149 Angle : 0.506 5.001 31136 Z= 0.272 Chirality : 0.043 0.141 3560 Planarity : 0.004 0.037 3936 Dihedral : 8.910 98.737 3673 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.93 % Allowed : 15.11 % Favored : 82.96 % 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: 0.78 (0.15), residues: 2888 helix: 1.43 (0.15), residues: 1224 sheet: 0.51 (0.32), residues: 248 loop : -0.22 (0.16), residues: 1416 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 D 57 ********************** 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 406 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 361 time to evaluate : 2.662 Fit side-chains outliers start: 45 outliers final: 40 residues processed: 392 average time/residue: 1.5921 time to fit residues: 697.1243 Evaluate side-chains 396 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 356 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN 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 260 LEU 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 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 260 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 277 GLN 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: 6.9990 chunk 243 optimal weight: 8.9990 chunk 69 optimal weight: 0.0770 chunk 210 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5940 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.157571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131370 restraints weight = 15484.802| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 0.88 r_work: 0.3329 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23008 Z= 0.116 Angle : 0.445 4.603 31136 Z= 0.239 Chirality : 0.040 0.143 3560 Planarity : 0.003 0.035 3936 Dihedral : 8.220 87.114 3664 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.80 % Allowed : 15.24 % Favored : 82.96 % 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: 1.00 (0.16), residues: 2888 helix: 1.55 (0.15), residues: 1224 sheet: 0.66 (0.28), residues: 360 loop : -0.13 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 93 PHE 0.007 0.001 PHE B 490 TYR 0.006 0.001 TYR A 353 ARG 0.001 0.000 ARG C 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10693.65 seconds wall clock time: 189 minutes 18.73 seconds (11358.73 seconds total)