Starting phenix.real_space_refine on Mon Jun 24 23:33:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj4_38393/06_2024/8xj4_38393.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj4_38393/06_2024/8xj4_38393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj4_38393/06_2024/8xj4_38393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj4_38393/06_2024/8xj4_38393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj4_38393/06_2024/8xj4_38393.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xj4_38393/06_2024/8xj4_38393.pdb" } resolution = 3.19 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= 0.035 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 32 5.16 5 C 3736 2.51 5 N 941 2.21 5 O 1111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 34": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 151": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 354": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 5820 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2834 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 25, 'TRANS': 321} Chain: "A" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2826 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 25, 'TRANS': 320} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.92, per 1000 atoms: 0.67 Number of scatterers: 5820 At special positions: 0 Unit cell: (89.1, 106.7, 74.8, 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 32 16.00 O 1111 8.00 N 941 7.00 C 3736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 372 " distance=2.04 Simple disulfide: pdb=" SG CYS A 347 " - pdb=" SG CYS A 351 " distance=2.03 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 Links applied ALPHA1-2 " MAN D 3 " - " MAN D 4 " ALPHA1-3 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 401 " - " ASN A 94 " " NAG A 402 " - " ASN A 220 " " NAG B 401 " - " ASN B 94 " " NAG B 403 " - " ASN B 220 " " NAG C 1 " - " ASN B 333 " " NAG D 1 " - " ASN A 333 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 50.6% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 59 through 63 removed outlier: 3.502A pdb=" N SER B 62 " --> pdb=" O LYS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.588A pdb=" N MET B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 124 removed outlier: 3.508A pdb=" N LEU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.911A pdb=" N ILE B 131 " --> pdb=" O GLY B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.536A pdb=" N GLN B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.615A pdb=" N GLN B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 removed outlier: 3.636A pdb=" N ALA B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 228 through 248 removed outlier: 4.061A pdb=" N TYR B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.691A pdb=" N VAL B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 301 removed outlier: 3.561A pdb=" N VAL B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 367 through 373 Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 109 through 124 removed outlier: 3.508A pdb=" N LEU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.521A pdb=" N SER A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 131 " --> pdb=" O GLY A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 161 through 174 removed outlier: 3.918A pdb=" N GLN A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 3.581A pdb=" N GLN A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 removed outlier: 3.701A pdb=" N ALA A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 228 through 248 removed outlier: 4.068A pdb=" N TYR A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 260 through 277 removed outlier: 3.684A pdb=" N VAL A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.524A pdb=" N VAL A 293 " --> pdb=" O HIS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.535A pdb=" N GLU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.539A pdb=" N HIS B 144 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR B 103 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER B 287 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG B 105 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE B 284 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 38 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 286 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 40 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 318 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 38 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 316 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 40 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS B 314 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 145 removed outlier: 3.539A pdb=" N HIS B 144 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR B 103 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER B 287 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG B 105 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE B 284 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 38 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 286 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 40 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 318 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 38 " --> pdb=" O THR B 316 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR B 316 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU B 40 " --> pdb=" O HIS B 314 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS B 314 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 327 " --> pdb=" O CYS B 351 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS B 351 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.684A pdb=" N TYR A 103 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER A 287 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG A 105 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE A 284 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 38 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N TYR A 286 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 40 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 318 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 38 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A 316 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU A 40 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N HIS A 314 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET A 329 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 102 through 105 removed outlier: 6.684A pdb=" N TYR A 103 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER A 287 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG A 105 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE A 284 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 38 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N TYR A 286 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 40 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 318 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 38 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR A 316 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU A 40 " --> pdb=" O HIS A 314 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N HIS A 314 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 327 " --> pdb=" O CYS A 351 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS A 351 " --> pdb=" O VAL A 327 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 774 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: 1.63 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1366 1.33 - 1.45: 1337 1.45 - 1.58: 3229 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 5984 Sorted by residual: bond pdb=" C1 NAG A 401 " pdb=" O5 NAG A 401 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N LEU A 156 " pdb=" CA LEU A 156 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.30e+00 bond pdb=" N LEU A 153 " pdb=" CA LEU A 153 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.26e-02 6.30e+03 8.24e+00 bond pdb=" N GLN B 101 " pdb=" CA GLN B 101 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.33e-02 5.65e+03 6.92e+00 ... (remaining 5979 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.16: 277 107.16 - 113.88: 3326 113.88 - 120.60: 2525 120.60 - 127.33: 1916 127.33 - 134.05: 87 Bond angle restraints: 8131 Sorted by residual: angle pdb=" N GLY B 248 " pdb=" CA GLY B 248 " pdb=" C GLY B 248 " ideal model delta sigma weight residual 113.18 122.85 -9.67 2.37e+00 1.78e-01 1.67e+01 angle pdb=" C PRO A 162 " pdb=" CA PRO A 162 " pdb=" CB PRO A 162 " ideal model delta sigma weight residual 112.62 106.12 6.50 1.65e+00 3.67e-01 1.55e+01 angle pdb=" C CYS A 161 " pdb=" N PRO A 162 " pdb=" CA PRO A 162 " ideal model delta sigma weight residual 119.05 123.25 -4.20 1.11e+00 8.12e-01 1.43e+01 angle pdb=" N GLY A 248 " pdb=" CA GLY A 248 " pdb=" C GLY A 248 " ideal model delta sigma weight residual 113.18 122.02 -8.84 2.37e+00 1.78e-01 1.39e+01 angle pdb=" CA SER B 96 " pdb=" C SER B 96 " pdb=" O SER B 96 " ideal model delta sigma weight residual 121.87 117.66 4.21 1.16e+00 7.43e-01 1.32e+01 ... (remaining 8126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.58: 3437 24.58 - 49.16: 236 49.16 - 73.75: 53 73.75 - 98.33: 24 98.33 - 122.91: 17 Dihedral angle restraints: 3767 sinusoidal: 1724 harmonic: 2043 Sorted by residual: dihedral pdb=" CD ARG A 159 " pdb=" NE ARG A 159 " pdb=" CZ ARG A 159 " pdb=" NH1 ARG A 159 " ideal model delta sinusoidal sigma weight residual 0.00 -75.83 75.83 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS B 347 " pdb=" SG CYS B 347 " pdb=" SG CYS B 351 " pdb=" CB CYS B 351 " ideal model delta sinusoidal sigma weight residual 93.00 140.40 -47.40 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N ASN B 220 " pdb=" CA ASN B 220 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 3764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 794 0.064 - 0.129: 101 0.129 - 0.193: 15 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 913 Sorted by residual: chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 94 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C1 NAG B 403 " pdb=" ND2 ASN B 220 " pdb=" C2 NAG B 403 " pdb=" O5 NAG B 403 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2 MAN D 3 " pdb=" C1 MAN D 3 " pdb=" C3 MAN D 3 " pdb=" O2 MAN D 3 " both_signs ideal model delta sigma weight residual False 2.52 2.71 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 910 not shown) Planarity restraints: 1025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 159 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG A 159 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 159 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 159 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 159 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 163 " 0.551 9.50e-02 1.11e+02 2.47e-01 3.73e+01 pdb=" NE ARG A 163 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 163 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 163 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 163 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 223 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 224 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " -0.036 5.00e-02 4.00e+02 ... (remaining 1022 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 890 2.76 - 3.29: 5531 3.29 - 3.83: 8992 3.83 - 4.36: 9947 4.36 - 4.90: 17912 Nonbonded interactions: 43272 Sorted by model distance: nonbonded pdb=" OH TYR B 89 " pdb=" OE2 GLU B 317 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR A 89 " pdb=" OE2 GLU A 317 " model vdw 2.357 2.440 nonbonded pdb=" O GLU B 166 " pdb=" OG SER B 169 " model vdw 2.380 2.440 nonbonded pdb=" O GLU A 166 " pdb=" OG SER A 169 " model vdw 2.396 2.440 nonbonded pdb=" O GLU A 168 " pdb=" OG1 THR A 171 " model vdw 2.408 2.440 ... (remaining 43267 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' and (resid 32 through 377 or resid 401)) selection = (chain 'B' and (resid 32 through 377 or resid 401)) } 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: 0.450 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: 1.950 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.920 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.005 0.079 5984 Z= 0.324 Angle : 0.797 9.674 8131 Z= 0.445 Chirality : 0.047 0.322 913 Planarity : 0.018 0.478 1019 Dihedral : 19.960 122.909 2441 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.57 % Allowed : 1.42 % Favored : 97.01 % 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: 1.21 (0.33), residues: 689 helix: 2.28 (0.31), residues: 307 sheet: 0.85 (0.53), residues: 76 loop : -0.77 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 206 HIS 0.005 0.001 HIS A 337 PHE 0.012 0.002 PHE A 356 TYR 0.016 0.001 TYR A 319 ARG 0.005 0.001 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8335 (mttp) REVERT: B 170 GLU cc_start: 0.7675 (tp30) cc_final: 0.7308 (tp30) REVERT: B 184 TYR cc_start: 0.6229 (p90) cc_final: 0.5922 (p90) outliers start: 10 outliers final: 3 residues processed: 87 average time/residue: 0.1829 time to fit residues: 20.8399 Evaluate side-chains 57 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 156 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 GLN B 304 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5984 Z= 0.275 Angle : 0.686 9.223 8131 Z= 0.334 Chirality : 0.046 0.207 913 Planarity : 0.006 0.061 1019 Dihedral : 17.948 109.984 1025 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.89 % Allowed : 7.56 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.33), residues: 689 helix: 2.24 (0.30), residues: 315 sheet: 0.74 (0.54), residues: 76 loop : -0.81 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.003 0.001 HIS B 314 PHE 0.016 0.002 PHE A 158 TYR 0.020 0.001 TYR A 184 ARG 0.003 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8411 (mtpt) REVERT: B 170 GLU cc_start: 0.7794 (tp30) cc_final: 0.7457 (tm-30) REVERT: B 184 TYR cc_start: 0.5959 (p90) cc_final: 0.5710 (p90) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.1747 time to fit residues: 15.2310 Evaluate side-chains 54 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 359 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5984 Z= 0.156 Angle : 0.632 8.468 8131 Z= 0.300 Chirality : 0.043 0.229 913 Planarity : 0.005 0.053 1019 Dihedral : 16.941 109.500 1023 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.20 % Allowed : 10.39 % Favored : 87.40 % 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: 1.52 (0.33), residues: 689 helix: 2.54 (0.30), residues: 316 sheet: 0.90 (0.54), residues: 76 loop : -0.70 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.003 0.001 HIS A 78 PHE 0.011 0.001 PHE A 53 TYR 0.029 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8292 (mtmt) REVERT: B 170 GLU cc_start: 0.7774 (tp30) cc_final: 0.7432 (tm-30) REVERT: B 184 TYR cc_start: 0.5793 (p90) cc_final: 0.5523 (p90) REVERT: A 161 CYS cc_start: 0.5862 (p) cc_final: 0.5653 (p) outliers start: 14 outliers final: 7 residues processed: 67 average time/residue: 0.2366 time to fit residues: 21.1388 Evaluate side-chains 55 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 65 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 37 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5984 Z= 0.159 Angle : 0.617 8.051 8131 Z= 0.292 Chirality : 0.043 0.255 913 Planarity : 0.006 0.053 1019 Dihedral : 16.036 110.892 1021 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.89 % Allowed : 13.07 % Favored : 85.04 % 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: 1.71 (0.33), residues: 689 helix: 2.67 (0.30), residues: 317 sheet: 0.95 (0.54), residues: 76 loop : -0.56 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.003 0.001 HIS A 78 PHE 0.010 0.001 PHE A 53 TYR 0.029 0.001 TYR A 184 ARG 0.003 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8267 (mtmt) REVERT: B 170 GLU cc_start: 0.7819 (tp30) cc_final: 0.7491 (tm-30) REVERT: B 184 TYR cc_start: 0.6001 (p90) cc_final: 0.5780 (p90) REVERT: B 373 MET cc_start: 0.6798 (tmm) cc_final: 0.6575 (tmm) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 0.1733 time to fit residues: 15.2988 Evaluate side-chains 56 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 chunk 12 optimal weight: 2.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 HIS ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5984 Z= 0.153 Angle : 0.619 8.175 8131 Z= 0.290 Chirality : 0.043 0.257 913 Planarity : 0.006 0.051 1019 Dihedral : 15.209 112.109 1019 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.57 % Allowed : 13.86 % Favored : 84.57 % 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: 1.82 (0.33), residues: 689 helix: 2.71 (0.30), residues: 319 sheet: 1.00 (0.53), residues: 76 loop : -0.45 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.003 0.001 HIS B 219 PHE 0.009 0.001 PHE A 53 TYR 0.031 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (mtmt) REVERT: B 170 GLU cc_start: 0.7937 (tp30) cc_final: 0.7525 (tm-30) REVERT: B 184 TYR cc_start: 0.5950 (p90) cc_final: 0.5706 (p90) REVERT: B 373 MET cc_start: 0.6798 (tmm) cc_final: 0.6510 (tmm) REVERT: A 170 GLU cc_start: 0.6880 (tp30) cc_final: 0.6489 (tm-30) outliers start: 10 outliers final: 7 residues processed: 59 average time/residue: 0.1660 time to fit residues: 13.5393 Evaluate side-chains 58 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5984 Z= 0.197 Angle : 0.634 8.387 8131 Z= 0.296 Chirality : 0.043 0.257 913 Planarity : 0.006 0.061 1019 Dihedral : 14.682 112.175 1019 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.52 % Allowed : 13.54 % Favored : 83.94 % 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: 1.74 (0.34), residues: 689 helix: 2.68 (0.30), residues: 319 sheet: 0.93 (0.54), residues: 76 loop : -0.54 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 226 HIS 0.002 0.001 HIS B 314 PHE 0.011 0.001 PHE A 158 TYR 0.024 0.001 TYR A 184 ARG 0.002 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8197 (mtmt) REVERT: B 170 GLU cc_start: 0.7946 (tp30) cc_final: 0.7536 (tm-30) REVERT: A 170 GLU cc_start: 0.6876 (tp30) cc_final: 0.6479 (tm-30) outliers start: 16 outliers final: 9 residues processed: 64 average time/residue: 0.1771 time to fit residues: 15.4120 Evaluate side-chains 60 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.0270 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5984 Z= 0.159 Angle : 0.630 8.405 8131 Z= 0.292 Chirality : 0.042 0.262 913 Planarity : 0.006 0.059 1019 Dihedral : 14.255 112.140 1019 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.73 % Allowed : 14.80 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.34), residues: 689 helix: 2.74 (0.30), residues: 319 sheet: 1.11 (0.56), residues: 76 loop : -0.43 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.007 0.001 PHE A 53 TYR 0.025 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8138 (mtmt) REVERT: B 156 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6748 (mm) REVERT: B 170 GLU cc_start: 0.7933 (tp30) cc_final: 0.7481 (tm-30) REVERT: A 170 GLU cc_start: 0.6930 (tp30) cc_final: 0.6533 (tm-30) REVERT: A 178 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7901 (mm-40) outliers start: 11 outliers final: 7 residues processed: 62 average time/residue: 0.1785 time to fit residues: 15.3090 Evaluate side-chains 60 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5984 Z= 0.194 Angle : 0.656 8.521 8131 Z= 0.303 Chirality : 0.043 0.255 913 Planarity : 0.006 0.059 1019 Dihedral : 13.856 111.785 1019 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.73 % Allowed : 14.80 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.34), residues: 689 helix: 2.68 (0.30), residues: 319 sheet: 0.98 (0.55), residues: 76 loop : -0.51 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 226 HIS 0.002 0.001 HIS A 78 PHE 0.011 0.001 PHE A 356 TYR 0.024 0.001 TYR A 184 ARG 0.001 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8076 (mtmt) REVERT: B 156 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6807 (mm) REVERT: B 170 GLU cc_start: 0.7946 (tp30) cc_final: 0.7494 (tm-30) REVERT: A 170 GLU cc_start: 0.6946 (tp30) cc_final: 0.6545 (tm-30) outliers start: 11 outliers final: 8 residues processed: 59 average time/residue: 0.1743 time to fit residues: 14.1514 Evaluate side-chains 59 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5984 Z= 0.185 Angle : 0.656 9.710 8131 Z= 0.303 Chirality : 0.043 0.262 913 Planarity : 0.006 0.059 1019 Dihedral : 13.399 111.293 1019 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.05 % Allowed : 14.80 % Favored : 83.15 % 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: 1.75 (0.34), residues: 689 helix: 2.68 (0.30), residues: 319 sheet: 0.97 (0.55), residues: 76 loop : -0.53 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 226 HIS 0.003 0.001 HIS B 270 PHE 0.008 0.001 PHE A 356 TYR 0.025 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6865 (mm) REVERT: B 170 GLU cc_start: 0.7957 (tp30) cc_final: 0.7687 (tp30) REVERT: A 170 GLU cc_start: 0.6872 (tp30) cc_final: 0.6489 (tm-30) REVERT: A 178 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7951 (mm-40) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 0.1734 time to fit residues: 13.5422 Evaluate side-chains 57 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5984 Z= 0.242 Angle : 0.692 10.354 8131 Z= 0.324 Chirality : 0.044 0.256 913 Planarity : 0.006 0.058 1019 Dihedral : 12.760 110.650 1015 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.42 % Allowed : 15.12 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.34), residues: 689 helix: 2.62 (0.30), residues: 317 sheet: 0.77 (0.55), residues: 76 loop : -0.70 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 226 HIS 0.003 0.001 HIS B 219 PHE 0.012 0.001 PHE B 158 TYR 0.023 0.001 TYR A 184 ARG 0.002 0.000 ARG B 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7028 (mm) REVERT: B 170 GLU cc_start: 0.7980 (tp30) cc_final: 0.7696 (tp30) REVERT: A 170 GLU cc_start: 0.6917 (tp30) cc_final: 0.6524 (tm-30) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1689 time to fit residues: 13.2040 Evaluate side-chains 56 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.0770 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 HIS ** 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 = 0.3742 r_free = 0.3742 target = 0.137051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102203 restraints weight = 8702.702| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.20 r_work: 0.3176 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5984 Z= 0.180 Angle : 0.649 10.502 8131 Z= 0.303 Chirality : 0.043 0.261 913 Planarity : 0.005 0.051 1019 Dihedral : 12.032 110.144 1015 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.26 % Allowed : 15.75 % Favored : 82.99 % 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: 1.68 (0.34), residues: 689 helix: 2.65 (0.30), residues: 319 sheet: 0.89 (0.55), residues: 76 loop : -0.59 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 226 HIS 0.002 0.001 HIS B 78 PHE 0.007 0.001 PHE A 356 TYR 0.025 0.001 TYR A 184 ARG 0.002 0.000 ARG B 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.98 seconds wall clock time: 26 minutes 16.79 seconds (1576.79 seconds total)