Starting phenix.real_space_refine on Fri Mar 15 18:26:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0x_20555/03_2024/6q0x_20555.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0x_20555/03_2024/6q0x_20555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0x_20555/03_2024/6q0x_20555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0x_20555/03_2024/6q0x_20555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0x_20555/03_2024/6q0x_20555.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q0x_20555/03_2024/6q0x_20555.pdb" } resolution = 4.2 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= -0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7984 2.51 5 N 2172 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 175": "OD1" <-> "OD2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C ASP 256": "OD1" <-> "OD2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C GLU 419": "OE1" <-> "OE2" Residue "C GLU 463": "OE1" <-> "OE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 175": "OD1" <-> "OD2" Residue "D TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D ASP 256": "OD1" <-> "OD2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 495": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12468 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3117 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "B" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3117 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3117 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "D" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3117 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 12, 'TRANS': 360} Time building chain proxies: 6.68, per 1000 atoms: 0.54 Number of scatterers: 12468 At special positions: 0 Unit cell: (81.312, 87.648, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2264 8.00 N 2172 7.00 C 7984 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: 5.41 Conformation dependent library (CDL) restraints added in 2.2 seconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 73.5% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 207 through 227 removed outlier: 4.296A pdb=" N ARG A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.098A pdb=" N LEU A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.648A pdb=" N THR A 257 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 330 removed outlier: 3.991A pdb=" N SER A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 421 removed outlier: 3.712A pdb=" N ASP A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 4.809A pdb=" N PHE A 382 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 501 removed outlier: 3.963A pdb=" N CYS A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 466 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 472 " --> pdb=" O GLN A 468 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 501 " --> pdb=" O GLU A 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 207 through 227 removed outlier: 4.296A pdb=" N ARG B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 241 removed outlier: 4.098A pdb=" N LEU B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.648A pdb=" N THR B 257 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 330 removed outlier: 3.991A pdb=" N SER B 287 " --> pdb=" O ASN B 283 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 421 removed outlier: 3.711A pdb=" N ASP B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Proline residue: B 377 - end of helix removed outlier: 4.809A pdb=" N PHE B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 501 removed outlier: 3.964A pdb=" N CYS B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE B 472 " --> pdb=" O GLN B 468 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B 475 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 Processing helix chain 'C' and resid 207 through 227 removed outlier: 4.295A pdb=" N ARG C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 241 removed outlier: 4.098A pdb=" N LEU C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.648A pdb=" N THR C 257 " --> pdb=" O THR C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 330 removed outlier: 3.990A pdb=" N SER C 287 " --> pdb=" O ASN C 283 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 421 removed outlier: 3.712A pdb=" N ASP C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Proline residue: C 377 - end of helix removed outlier: 4.809A pdb=" N PHE C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 383 " --> pdb=" O PHE C 379 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 501 removed outlier: 3.965A pdb=" N CYS C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE C 466 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE C 472 " --> pdb=" O GLN C 468 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 475 " --> pdb=" O GLN C 471 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR C 501 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 187 Processing helix chain 'D' and resid 207 through 227 removed outlier: 4.295A pdb=" N ARG D 213 " --> pdb=" O PHE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 241 removed outlier: 4.098A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 254 through 258 removed outlier: 3.648A pdb=" N THR D 257 " --> pdb=" O THR D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 330 removed outlier: 3.991A pdb=" N SER D 287 " --> pdb=" O ASN D 283 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 421 removed outlier: 3.712A pdb=" N ASP D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Proline residue: D 377 - end of helix removed outlier: 4.809A pdb=" N PHE D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR D 383 " --> pdb=" O PHE D 379 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN D 403 " --> pdb=" O MET D 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 501 removed outlier: 3.963A pdb=" N CYS D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE D 472 " --> pdb=" O GLN D 468 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR D 475 " --> pdb=" O GLN D 471 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR D 501 " --> pdb=" O GLU D 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 137 removed outlier: 6.000A pdb=" N ILE A 133 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LYS A 153 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU A 135 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU A 151 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 132 through 137 removed outlier: 6.000A pdb=" N ILE B 133 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LYS B 153 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLU B 135 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 151 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 132 through 137 removed outlier: 6.001A pdb=" N ILE C 133 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LYS C 153 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU C 135 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU C 151 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 132 through 137 removed outlier: 6.001A pdb=" N ILE D 133 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LYS D 153 " --> pdb=" O ILE D 133 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU D 135 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU D 151 " --> pdb=" O GLU D 135 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2676 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: 3.54 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4050 1.34 - 1.46: 2433 1.46 - 1.58: 6149 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 12716 Sorted by residual: bond pdb=" CB GLU A 307 " pdb=" CG GLU A 307 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.50e+00 bond pdb=" CB GLU B 307 " pdb=" CG GLU B 307 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 bond pdb=" CB GLU D 307 " pdb=" CG GLU D 307 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CB GLU C 307 " pdb=" CG GLU C 307 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" CB VAL B 314 " pdb=" CG1 VAL B 314 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 ... (remaining 12711 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.87: 316 106.87 - 113.68: 7394 113.68 - 120.49: 5134 120.49 - 127.30: 4155 127.30 - 134.11: 137 Bond angle restraints: 17136 Sorted by residual: angle pdb=" C GLU B 165 " pdb=" N GLU B 166 " pdb=" CA GLU B 166 " ideal model delta sigma weight residual 121.54 130.50 -8.96 1.91e+00 2.74e-01 2.20e+01 angle pdb=" C GLU C 165 " pdb=" N GLU C 166 " pdb=" CA GLU C 166 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 angle pdb=" C GLU A 165 " pdb=" N GLU A 166 " pdb=" CA GLU A 166 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C GLU D 165 " pdb=" N GLU D 166 " pdb=" CA GLU D 166 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 angle pdb=" N THR D 161 " pdb=" CA THR D 161 " pdb=" C THR D 161 " ideal model delta sigma weight residual 109.46 102.91 6.55 1.66e+00 3.63e-01 1.56e+01 ... (remaining 17131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 6677 17.91 - 35.81: 964 35.81 - 53.72: 147 53.72 - 71.63: 24 71.63 - 89.53: 32 Dihedral angle restraints: 7844 sinusoidal: 3396 harmonic: 4448 Sorted by residual: dihedral pdb=" CA SER B 160 " pdb=" C SER B 160 " pdb=" N THR B 161 " pdb=" CA THR B 161 " ideal model delta harmonic sigma weight residual 180.00 149.54 30.46 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA SER C 160 " pdb=" C SER C 160 " pdb=" N THR C 161 " pdb=" CA THR C 161 " ideal model delta harmonic sigma weight residual 180.00 149.55 30.45 0 5.00e+00 4.00e-02 3.71e+01 dihedral pdb=" CA SER A 160 " pdb=" C SER A 160 " pdb=" N THR A 161 " pdb=" CA THR A 161 " ideal model delta harmonic sigma weight residual 180.00 149.60 30.40 0 5.00e+00 4.00e-02 3.70e+01 ... (remaining 7841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1049 0.032 - 0.064: 561 0.064 - 0.096: 226 0.096 - 0.128: 69 0.128 - 0.160: 11 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CA TRP C 282 " pdb=" N TRP C 282 " pdb=" C TRP C 282 " pdb=" CB TRP C 282 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA TRP D 282 " pdb=" N TRP D 282 " pdb=" C TRP D 282 " pdb=" CB TRP D 282 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA TRP B 282 " pdb=" N TRP B 282 " pdb=" C TRP B 282 " pdb=" CB TRP B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1913 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 368 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C THR B 368 " 0.033 2.00e-02 2.50e+03 pdb=" O THR B 368 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU B 369 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 368 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C THR D 368 " -0.033 2.00e-02 2.50e+03 pdb=" O THR D 368 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D 369 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 368 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C THR A 368 " 0.033 2.00e-02 2.50e+03 pdb=" O THR A 368 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 369 " -0.011 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 441 2.69 - 3.24: 14469 3.24 - 3.80: 21173 3.80 - 4.35: 26479 4.35 - 4.90: 40579 Nonbonded interactions: 103141 Sorted by model distance: nonbonded pdb=" OH TYR C 335 " pdb=" OG1 THR D 470 " model vdw 2.139 2.440 nonbonded pdb=" NH1 ARG D 186 " pdb=" O ASN D 259 " model vdw 2.140 2.520 nonbonded pdb=" NH1 ARG C 186 " pdb=" O ASN C 259 " model vdw 2.140 2.520 nonbonded pdb=" NH1 ARG A 186 " pdb=" O ASN A 259 " model vdw 2.141 2.520 nonbonded pdb=" NH1 ARG B 186 " pdb=" O ASN B 259 " model vdw 2.141 2.520 ... (remaining 103136 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' } 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 group one per residue 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.550 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 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 0.055 12716 Z= 0.452 Angle : 0.879 9.204 17136 Z= 0.496 Chirality : 0.045 0.160 1916 Planarity : 0.005 0.032 2160 Dihedral : 17.073 89.531 4916 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.21 % Allowed : 13.79 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.83 (0.17), residues: 1484 helix: -2.03 (0.12), residues: 1032 sheet: None (None), residues: 0 loop : -3.45 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 249 HIS 0.006 0.002 HIS D 306 PHE 0.025 0.002 PHE D 467 TYR 0.015 0.002 TYR B 297 ARG 0.004 0.001 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 427 time to evaluate : 1.564 Fit side-chains REVERT: A 224 VAL cc_start: 0.9290 (t) cc_final: 0.8839 (t) REVERT: A 225 MET cc_start: 0.7569 (mmm) cc_final: 0.7341 (tpp) REVERT: A 226 LYS cc_start: 0.4613 (tptm) cc_final: 0.3675 (tptp) REVERT: A 260 GLU cc_start: 0.7171 (tp30) cc_final: 0.6415 (tm-30) REVERT: A 294 GLU cc_start: 0.7548 (tt0) cc_final: 0.7148 (tt0) REVERT: A 306 HIS cc_start: 0.8065 (m-70) cc_final: 0.7851 (m-70) REVERT: A 330 VAL cc_start: 0.8236 (m) cc_final: 0.7991 (m) REVERT: A 337 VAL cc_start: 0.8430 (m) cc_final: 0.8193 (p) REVERT: A 375 LEU cc_start: 0.8530 (tt) cc_final: 0.8013 (tt) REVERT: A 392 LEU cc_start: 0.8730 (mt) cc_final: 0.8254 (tt) REVERT: A 393 PHE cc_start: 0.7974 (m-10) cc_final: 0.7757 (m-80) REVERT: A 409 ARG cc_start: 0.7805 (ttt180) cc_final: 0.7496 (ttt180) REVERT: B 224 VAL cc_start: 0.9286 (t) cc_final: 0.8686 (t) REVERT: B 226 LYS cc_start: 0.4639 (tptm) cc_final: 0.4405 (tptt) REVERT: B 321 GLU cc_start: 0.7865 (tt0) cc_final: 0.7658 (tt0) REVERT: B 330 VAL cc_start: 0.8158 (m) cc_final: 0.7903 (m) REVERT: B 337 VAL cc_start: 0.8396 (m) cc_final: 0.8095 (p) REVERT: B 347 ASN cc_start: 0.8457 (p0) cc_final: 0.7969 (p0) REVERT: B 375 LEU cc_start: 0.8487 (tt) cc_final: 0.7973 (tt) REVERT: B 392 LEU cc_start: 0.8729 (mt) cc_final: 0.8201 (tt) REVERT: B 409 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7536 (ttt180) REVERT: C 224 VAL cc_start: 0.9292 (t) cc_final: 0.8899 (t) REVERT: C 225 MET cc_start: 0.7553 (mmm) cc_final: 0.7314 (tpp) REVERT: C 226 LYS cc_start: 0.4770 (tptm) cc_final: 0.3793 (tptp) REVERT: C 260 GLU cc_start: 0.7356 (tp30) cc_final: 0.6550 (tm-30) REVERT: C 306 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7813 (m-70) REVERT: C 307 GLU cc_start: 0.7062 (tp30) cc_final: 0.6846 (tp30) REVERT: C 330 VAL cc_start: 0.8237 (m) cc_final: 0.7998 (m) REVERT: C 337 VAL cc_start: 0.8410 (m) cc_final: 0.8146 (p) REVERT: C 375 LEU cc_start: 0.8497 (tt) cc_final: 0.7971 (tt) REVERT: C 392 LEU cc_start: 0.8760 (mt) cc_final: 0.8266 (tt) REVERT: C 393 PHE cc_start: 0.7964 (m-10) cc_final: 0.7744 (m-80) REVERT: C 409 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7520 (ttt180) REVERT: D 224 VAL cc_start: 0.9289 (t) cc_final: 0.8645 (t) REVERT: D 226 LYS cc_start: 0.4643 (tptm) cc_final: 0.4291 (tptt) REVERT: D 260 GLU cc_start: 0.7058 (tp30) cc_final: 0.6330 (tm-30) REVERT: D 330 VAL cc_start: 0.8269 (m) cc_final: 0.8014 (m) REVERT: D 337 VAL cc_start: 0.8429 (m) cc_final: 0.8122 (p) REVERT: D 375 LEU cc_start: 0.8526 (tt) cc_final: 0.8025 (tt) REVERT: D 392 LEU cc_start: 0.8749 (mt) cc_final: 0.8248 (tt) REVERT: D 393 PHE cc_start: 0.7970 (m-10) cc_final: 0.7762 (m-80) REVERT: D 409 ARG cc_start: 0.7822 (ttt180) cc_final: 0.7465 (ttt180) outliers start: 17 outliers final: 0 residues processed: 439 average time/residue: 0.2710 time to fit residues: 164.2874 Evaluate side-chains 291 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.4980 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 GLN ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12716 Z= 0.271 Angle : 0.736 8.823 17136 Z= 0.385 Chirality : 0.043 0.163 1916 Planarity : 0.005 0.047 2160 Dihedral : 6.024 28.362 1624 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.57 % Allowed : 4.64 % Favored : 94.79 % 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: -1.56 (0.20), residues: 1484 helix: -0.31 (0.15), residues: 1044 sheet: None (None), residues: 0 loop : -2.66 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 282 HIS 0.010 0.003 HIS C 154 PHE 0.023 0.003 PHE C 220 TYR 0.010 0.001 TYR A 297 ARG 0.009 0.001 ARG D 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 387 time to evaluate : 1.326 Fit side-chains REVERT: A 175 ASP cc_start: 0.7421 (m-30) cc_final: 0.6332 (m-30) REVERT: A 224 VAL cc_start: 0.9185 (t) cc_final: 0.8387 (t) REVERT: A 270 PHE cc_start: 0.6822 (t80) cc_final: 0.6524 (m-80) REVERT: A 337 VAL cc_start: 0.8395 (m) cc_final: 0.8049 (p) REVERT: A 392 LEU cc_start: 0.8820 (mt) cc_final: 0.8108 (tt) REVERT: A 409 ARG cc_start: 0.7654 (ttt180) cc_final: 0.7408 (ttt180) REVERT: B 175 ASP cc_start: 0.7161 (m-30) cc_final: 0.6284 (m-30) REVERT: B 224 VAL cc_start: 0.9102 (t) cc_final: 0.8422 (t) REVERT: B 226 LYS cc_start: 0.4172 (tptm) cc_final: 0.3287 (mtmm) REVERT: B 337 VAL cc_start: 0.8399 (m) cc_final: 0.8007 (p) REVERT: B 392 LEU cc_start: 0.8763 (mt) cc_final: 0.7974 (tt) REVERT: C 175 ASP cc_start: 0.7235 (m-30) cc_final: 0.6434 (m-30) REVERT: C 224 VAL cc_start: 0.9146 (t) cc_final: 0.8564 (t) REVERT: C 226 LYS cc_start: 0.4521 (tptm) cc_final: 0.3732 (mtmm) REVERT: C 270 PHE cc_start: 0.6844 (t80) cc_final: 0.6514 (m-80) REVERT: C 337 VAL cc_start: 0.8373 (m) cc_final: 0.7991 (p) REVERT: C 392 LEU cc_start: 0.8824 (mt) cc_final: 0.8044 (tt) REVERT: C 485 ASN cc_start: 0.8277 (t0) cc_final: 0.8048 (t0) REVERT: D 175 ASP cc_start: 0.7390 (m-30) cc_final: 0.6320 (m-30) REVERT: D 224 VAL cc_start: 0.9104 (t) cc_final: 0.8448 (t) REVERT: D 226 LYS cc_start: 0.4293 (tptm) cc_final: 0.3454 (mtmm) REVERT: D 270 PHE cc_start: 0.6895 (t80) cc_final: 0.6672 (m-80) REVERT: D 337 VAL cc_start: 0.8375 (m) cc_final: 0.8015 (p) REVERT: D 392 LEU cc_start: 0.8834 (mt) cc_final: 0.8070 (tt) outliers start: 8 outliers final: 0 residues processed: 391 average time/residue: 0.2561 time to fit residues: 140.7369 Evaluate side-chains 300 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 0.2980 chunk 145 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12716 Z= 0.351 Angle : 0.751 7.210 17136 Z= 0.405 Chirality : 0.042 0.150 1916 Planarity : 0.005 0.037 2160 Dihedral : 5.980 27.973 1624 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.64 % Allowed : 6.57 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1484 helix: 0.23 (0.15), residues: 1044 sheet: None (None), residues: 0 loop : -2.59 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 282 HIS 0.017 0.002 HIS C 227 PHE 0.035 0.003 PHE A 220 TYR 0.015 0.002 TYR D 150 ARG 0.006 0.001 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 330 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ARG cc_start: 0.7762 (ttm170) cc_final: 0.7410 (tpp80) REVERT: A 224 VAL cc_start: 0.9175 (t) cc_final: 0.8677 (t) REVERT: B 213 ARG cc_start: 0.7771 (ttm170) cc_final: 0.7452 (tpp80) REVERT: B 224 VAL cc_start: 0.9226 (t) cc_final: 0.8684 (t) REVERT: B 226 LYS cc_start: 0.4827 (tptm) cc_final: 0.4564 (tptt) REVERT: B 392 LEU cc_start: 0.8728 (mt) cc_final: 0.7967 (tt) REVERT: B 394 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6770 (mt-10) REVERT: C 213 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7435 (tpp80) REVERT: C 224 VAL cc_start: 0.9170 (t) cc_final: 0.8527 (t) REVERT: C 226 LYS cc_start: 0.4862 (tptm) cc_final: 0.4613 (tptt) REVERT: D 213 ARG cc_start: 0.7778 (ttm170) cc_final: 0.7394 (tpp80) REVERT: D 226 LYS cc_start: 0.4949 (tptm) cc_final: 0.4587 (tptt) outliers start: 9 outliers final: 0 residues processed: 338 average time/residue: 0.2711 time to fit residues: 126.9815 Evaluate side-chains 250 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN A 449 GLN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 281 GLN C 449 GLN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN D 449 GLN ** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12716 Z= 0.268 Angle : 0.681 7.078 17136 Z= 0.366 Chirality : 0.042 0.144 1916 Planarity : 0.004 0.031 2160 Dihedral : 5.766 26.754 1624 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.50 % Allowed : 4.21 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1484 helix: 0.62 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -2.23 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 274 HIS 0.014 0.002 HIS C 227 PHE 0.037 0.002 PHE D 220 TYR 0.011 0.001 TYR C 150 ARG 0.004 0.001 ARG D 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 339 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.7645 (tptp) cc_final: 0.7405 (tptp) REVERT: A 394 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6619 (mt-10) REVERT: A 484 LEU cc_start: 0.8104 (mt) cc_final: 0.7889 (mt) REVERT: B 191 MET cc_start: 0.4772 (pmm) cc_final: 0.4519 (pmm) REVERT: B 294 GLU cc_start: 0.6803 (tt0) cc_final: 0.6601 (tt0) REVERT: B 384 ASP cc_start: 0.7530 (m-30) cc_final: 0.7319 (t70) REVERT: C 224 VAL cc_start: 0.9232 (t) cc_final: 0.8671 (t) REVERT: C 226 LYS cc_start: 0.4647 (tptm) cc_final: 0.3815 (mtmm) REVERT: C 312 GLN cc_start: 0.7000 (tm-30) cc_final: 0.6733 (tm-30) REVERT: C 394 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6737 (mt-10) REVERT: D 224 VAL cc_start: 0.9230 (t) cc_final: 0.8793 (t) REVERT: D 394 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6751 (mt-10) outliers start: 7 outliers final: 0 residues processed: 346 average time/residue: 0.2764 time to fit residues: 131.2227 Evaluate side-chains 280 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 HIS ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 449 GLN ** C 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 GLN ** D 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12716 Z= 0.337 Angle : 0.733 7.694 17136 Z= 0.393 Chirality : 0.044 0.160 1916 Planarity : 0.005 0.057 2160 Dihedral : 5.825 26.749 1624 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.29 % Allowed : 4.21 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1484 helix: 0.60 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP D 282 HIS 0.021 0.002 HIS B 356 PHE 0.038 0.003 PHE B 220 TYR 0.011 0.002 TYR B 150 ARG 0.006 0.001 ARG D 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 322 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 224 VAL cc_start: 0.9221 (t) cc_final: 0.8727 (t) REVERT: A 394 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6704 (mt-10) REVERT: A 484 LEU cc_start: 0.8127 (mt) cc_final: 0.7921 (mt) REVERT: B 224 VAL cc_start: 0.9237 (t) cc_final: 0.8693 (t) REVERT: B 294 GLU cc_start: 0.6782 (tt0) cc_final: 0.6551 (tt0) REVERT: B 384 ASP cc_start: 0.7670 (m-30) cc_final: 0.7440 (t70) REVERT: B 394 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6668 (mt-10) REVERT: B 399 MET cc_start: 0.8131 (tpp) cc_final: 0.7903 (tpp) REVERT: C 224 VAL cc_start: 0.9199 (t) cc_final: 0.8712 (t) REVERT: C 226 LYS cc_start: 0.4852 (tptm) cc_final: 0.4452 (tptt) REVERT: C 368 THR cc_start: 0.7954 (p) cc_final: 0.7505 (p) REVERT: C 394 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6896 (mt-10) REVERT: D 294 GLU cc_start: 0.6829 (tt0) cc_final: 0.6548 (tt0) REVERT: D 394 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6846 (mt-10) outliers start: 4 outliers final: 0 residues processed: 326 average time/residue: 0.2440 time to fit residues: 112.4849 Evaluate side-chains 264 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN B 339 GLN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 339 GLN ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12716 Z= 0.231 Angle : 0.666 7.093 17136 Z= 0.353 Chirality : 0.042 0.168 1916 Planarity : 0.004 0.042 2160 Dihedral : 5.587 25.762 1624 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1484 helix: 0.92 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -2.39 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP B 282 HIS 0.018 0.002 HIS B 356 PHE 0.040 0.002 PHE B 220 TYR 0.012 0.001 TYR D 187 ARG 0.008 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLU cc_start: 0.6740 (tt0) cc_final: 0.6527 (tt0) REVERT: A 312 GLN cc_start: 0.7269 (tm-30) cc_final: 0.7020 (tm-30) REVERT: B 244 THR cc_start: 0.7468 (t) cc_final: 0.7149 (t) REVERT: B 309 ARG cc_start: 0.7450 (ttm-80) cc_final: 0.6924 (ttm-80) REVERT: B 394 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6679 (mt-10) REVERT: B 399 MET cc_start: 0.8113 (tpp) cc_final: 0.7845 (tpp) REVERT: C 224 VAL cc_start: 0.9147 (t) cc_final: 0.8937 (t) REVERT: C 226 LYS cc_start: 0.4421 (tptm) cc_final: 0.3862 (mtmm) REVERT: C 294 GLU cc_start: 0.6832 (tt0) cc_final: 0.6495 (tt0) REVERT: C 357 LEU cc_start: 0.8273 (mm) cc_final: 0.8064 (mm) REVERT: C 368 THR cc_start: 0.7683 (p) cc_final: 0.7418 (p) REVERT: D 226 LYS cc_start: 0.5118 (tptt) cc_final: 0.4118 (mtmm) REVERT: D 244 THR cc_start: 0.7354 (t) cc_final: 0.6885 (t) REVERT: D 294 GLU cc_start: 0.6707 (tt0) cc_final: 0.6478 (tt0) REVERT: D 384 ASP cc_start: 0.7005 (t70) cc_final: 0.6758 (t70) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2379 time to fit residues: 116.9920 Evaluate side-chains 274 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN B 339 GLN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN C 339 GLN ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12716 Z= 0.247 Angle : 0.684 7.097 17136 Z= 0.364 Chirality : 0.042 0.186 1916 Planarity : 0.005 0.067 2160 Dihedral : 5.549 26.291 1624 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -0.06 (0.22), residues: 1484 helix: 0.89 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.50 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP B 282 HIS 0.015 0.002 HIS C 227 PHE 0.044 0.002 PHE B 220 TYR 0.010 0.001 TYR B 173 ARG 0.005 0.001 ARG D 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.4752 (tptt) cc_final: 0.3606 (mtmm) REVERT: A 244 THR cc_start: 0.7158 (t) cc_final: 0.6559 (t) REVERT: A 357 LEU cc_start: 0.8438 (mm) cc_final: 0.8058 (mm) REVERT: A 394 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6381 (mt-10) REVERT: A 399 MET cc_start: 0.8057 (tpp) cc_final: 0.7759 (tpp) REVERT: B 226 LYS cc_start: 0.4804 (tptt) cc_final: 0.3879 (tptt) REVERT: B 309 ARG cc_start: 0.7307 (ttm-80) cc_final: 0.6990 (ttm-80) REVERT: B 311 MET cc_start: 0.6780 (tpt) cc_final: 0.6427 (tpt) REVERT: B 394 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6705 (mt-10) REVERT: B 399 MET cc_start: 0.8144 (tpp) cc_final: 0.7891 (tpp) REVERT: C 187 TYR cc_start: 0.8118 (m-80) cc_final: 0.7611 (m-80) REVERT: C 224 VAL cc_start: 0.9216 (t) cc_final: 0.8821 (t) REVERT: C 226 LYS cc_start: 0.4586 (tptm) cc_final: 0.4364 (tptt) REVERT: C 294 GLU cc_start: 0.6779 (tt0) cc_final: 0.6435 (tt0) REVERT: D 191 MET cc_start: 0.5032 (pmm) cc_final: 0.4687 (pmm) REVERT: D 226 LYS cc_start: 0.5262 (tptt) cc_final: 0.4622 (tptt) REVERT: D 294 GLU cc_start: 0.6769 (tt0) cc_final: 0.6562 (tt0) REVERT: D 311 MET cc_start: 0.6972 (tpt) cc_final: 0.6552 (tpt) REVERT: D 312 GLN cc_start: 0.7272 (tm-30) cc_final: 0.6974 (tm-30) REVERT: D 357 LEU cc_start: 0.8311 (mm) cc_final: 0.7966 (mm) REVERT: D 394 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6921 (mt-10) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.2330 time to fit residues: 111.1886 Evaluate side-chains 268 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 0.0050 chunk 129 optimal weight: 2.9990 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** D 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12716 Z= 0.245 Angle : 0.683 7.018 17136 Z= 0.363 Chirality : 0.043 0.167 1916 Planarity : 0.005 0.067 2160 Dihedral : 5.463 25.670 1624 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -0.05 (0.22), residues: 1484 helix: 0.92 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.61 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP B 282 HIS 0.013 0.002 HIS C 227 PHE 0.045 0.003 PHE B 220 TYR 0.011 0.001 TYR D 173 ARG 0.005 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 THR cc_start: 0.7126 (t) cc_final: 0.6876 (t) REVERT: A 311 MET cc_start: 0.6812 (tpt) cc_final: 0.6496 (tpt) REVERT: A 370 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 392 LEU cc_start: 0.8527 (mt) cc_final: 0.8029 (tt) REVERT: A 399 MET cc_start: 0.8091 (tpp) cc_final: 0.7742 (tpp) REVERT: B 224 VAL cc_start: 0.9072 (t) cc_final: 0.8808 (t) REVERT: B 244 THR cc_start: 0.7239 (t) cc_final: 0.7005 (t) REVERT: B 392 LEU cc_start: 0.8506 (mt) cc_final: 0.8006 (tt) REVERT: B 399 MET cc_start: 0.8161 (tpp) cc_final: 0.7941 (tpp) REVERT: C 187 TYR cc_start: 0.8099 (m-80) cc_final: 0.7612 (m-80) REVERT: C 357 LEU cc_start: 0.8306 (mm) cc_final: 0.8038 (mm) REVERT: D 224 VAL cc_start: 0.9183 (t) cc_final: 0.8821 (t) REVERT: D 226 LYS cc_start: 0.5142 (tptt) cc_final: 0.4401 (tptp) REVERT: D 357 LEU cc_start: 0.8429 (mm) cc_final: 0.8117 (mm) REVERT: D 392 LEU cc_start: 0.8552 (mt) cc_final: 0.8009 (tt) REVERT: D 394 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6527 (mt-10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2412 time to fit residues: 119.8765 Evaluate side-chains 274 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 0.3980 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN D 147 HIS ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12716 Z= 0.227 Angle : 0.677 8.100 17136 Z= 0.357 Chirality : 0.042 0.248 1916 Planarity : 0.005 0.078 2160 Dihedral : 5.357 25.321 1624 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 0.15 (0.22), residues: 1484 helix: 1.11 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.70 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.004 TRP D 282 HIS 0.012 0.002 HIS B 315 PHE 0.046 0.002 PHE C 220 TYR 0.014 0.002 TYR D 173 ARG 0.005 0.000 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 VAL cc_start: 0.9080 (t) cc_final: 0.8705 (t) REVERT: A 311 MET cc_start: 0.6703 (tpt) cc_final: 0.6332 (tpt) REVERT: A 343 ILE cc_start: 0.8150 (mp) cc_final: 0.7899 (mt) REVERT: A 370 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7003 (mm-30) REVERT: A 392 LEU cc_start: 0.8363 (mt) cc_final: 0.7947 (tt) REVERT: A 394 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6538 (mt-10) REVERT: A 399 MET cc_start: 0.7976 (tpp) cc_final: 0.7628 (tpp) REVERT: B 226 LYS cc_start: 0.4904 (tptt) cc_final: 0.4511 (tptt) REVERT: B 244 THR cc_start: 0.7173 (t) cc_final: 0.6951 (t) REVERT: B 311 MET cc_start: 0.6353 (tpt) cc_final: 0.6047 (tpt) REVERT: B 392 LEU cc_start: 0.8440 (mt) cc_final: 0.7894 (tt) REVERT: B 394 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6379 (mt-10) REVERT: B 399 MET cc_start: 0.8123 (tpp) cc_final: 0.7843 (tpp) REVERT: C 187 TYR cc_start: 0.8172 (m-80) cc_final: 0.7635 (m-80) REVERT: C 224 VAL cc_start: 0.9169 (t) cc_final: 0.8868 (t) REVERT: C 311 MET cc_start: 0.6853 (tpt) cc_final: 0.6564 (tpt) REVERT: C 357 LEU cc_start: 0.8364 (mm) cc_final: 0.8089 (mm) REVERT: C 392 LEU cc_start: 0.8449 (mt) cc_final: 0.8012 (tt) REVERT: D 224 VAL cc_start: 0.9147 (t) cc_final: 0.8917 (t) REVERT: D 226 LYS cc_start: 0.5081 (tptt) cc_final: 0.4798 (tptt) REVERT: D 309 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.7135 (ttm-80) REVERT: D 311 MET cc_start: 0.6813 (tpt) cc_final: 0.6518 (tpt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2439 time to fit residues: 117.8165 Evaluate side-chains 275 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 4.9990 chunk 66 optimal weight: 0.0010 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 HIS ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 HIS ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12716 Z= 0.224 Angle : 0.701 8.553 17136 Z= 0.369 Chirality : 0.043 0.190 1916 Planarity : 0.005 0.069 2160 Dihedral : 5.284 24.413 1624 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 0.15 (0.22), residues: 1484 helix: 1.11 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.68 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.004 TRP D 282 HIS 0.011 0.002 HIS B 315 PHE 0.044 0.002 PHE D 220 TYR 0.016 0.001 TYR D 173 ARG 0.005 0.000 ARG C 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 LEU cc_start: 0.6970 (mm) cc_final: 0.6593 (mm) REVERT: A 311 MET cc_start: 0.6735 (tpt) cc_final: 0.6425 (tpt) REVERT: A 343 ILE cc_start: 0.8052 (mp) cc_final: 0.7346 (mt) REVERT: A 368 THR cc_start: 0.7729 (p) cc_final: 0.7286 (p) REVERT: A 370 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7013 (mm-30) REVERT: A 384 ASP cc_start: 0.6704 (t70) cc_final: 0.6314 (t70) REVERT: A 392 LEU cc_start: 0.8426 (mt) cc_final: 0.8006 (tt) REVERT: A 399 MET cc_start: 0.7965 (tpp) cc_final: 0.7590 (tpp) REVERT: B 177 LEU cc_start: 0.7009 (mm) cc_final: 0.6625 (mm) REVERT: B 309 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7070 (ttm-80) REVERT: B 311 MET cc_start: 0.6320 (tpt) cc_final: 0.6062 (tpt) REVERT: B 343 ILE cc_start: 0.8256 (mp) cc_final: 0.7957 (mp) REVERT: B 368 THR cc_start: 0.7781 (p) cc_final: 0.7303 (p) REVERT: B 392 LEU cc_start: 0.8411 (mt) cc_final: 0.7912 (tt) REVERT: B 394 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6549 (mt-10) REVERT: B 399 MET cc_start: 0.8029 (tpp) cc_final: 0.7784 (tpp) REVERT: C 187 TYR cc_start: 0.8116 (m-80) cc_final: 0.7750 (m-80) REVERT: C 226 LYS cc_start: 0.4763 (tptt) cc_final: 0.3765 (mtmm) REVERT: C 311 MET cc_start: 0.6734 (tpt) cc_final: 0.6444 (tpt) REVERT: C 343 ILE cc_start: 0.8246 (mp) cc_final: 0.7877 (mt) REVERT: C 357 LEU cc_start: 0.8360 (mm) cc_final: 0.8086 (mm) REVERT: C 392 LEU cc_start: 0.8406 (mt) cc_final: 0.8039 (tt) REVERT: D 177 LEU cc_start: 0.6986 (mm) cc_final: 0.6709 (mm) REVERT: D 226 LYS cc_start: 0.5199 (tptt) cc_final: 0.4192 (mtmm) REVERT: D 309 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7097 (ttm-80) REVERT: D 311 MET cc_start: 0.6839 (tpt) cc_final: 0.6500 (tpt) REVERT: D 312 GLN cc_start: 0.7331 (tm-30) cc_final: 0.7109 (tm-30) REVERT: D 343 ILE cc_start: 0.7977 (mp) cc_final: 0.7263 (mt) REVERT: D 368 THR cc_start: 0.7737 (p) cc_final: 0.7333 (p) REVERT: D 394 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6431 (mt-10) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2383 time to fit residues: 117.5601 Evaluate side-chains 277 residues out of total 1400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 0.0870 chunk 49 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 0.0010 chunk 6 optimal weight: 0.9990 overall best weight: 0.5966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.177691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.147764 restraints weight = 25217.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.151042 restraints weight = 16093.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.153333 restraints weight = 11675.866| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12716 Z= 0.233 Angle : 0.697 8.842 17136 Z= 0.371 Chirality : 0.043 0.190 1916 Planarity : 0.005 0.068 2160 Dihedral : 5.175 23.840 1624 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.22), residues: 1484 helix: 1.08 (0.16), residues: 1072 sheet: None (None), residues: 0 loop : -2.72 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.004 TRP D 282 HIS 0.011 0.001 HIS C 227 PHE 0.044 0.002 PHE C 220 TYR 0.015 0.001 TYR D 173 ARG 0.005 0.000 ARG C 309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.48 seconds wall clock time: 51 minutes 15.67 seconds (3075.67 seconds total)