Starting phenix.real_space_refine on Thu Mar 14 23:15:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/03_2024/6wun_21917.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/03_2024/6wun_21917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/03_2024/6wun_21917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/03_2024/6wun_21917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/03_2024/6wun_21917.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wun_21917/03_2024/6wun_21917.pdb" } resolution = 3.9 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= 0.023 sd= 0.112 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 16 5.16 5 C 6370 2.51 5 N 1814 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 58": "OD1" <-> "OD2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C GLU 258": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 394": "OD1" <-> "OD2" Residue "D ASP 436": "OD1" <-> "OD2" Residue "D ARG 482": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10082 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2044 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 21, 'TRANS': 238} Chain breaks: 4 Chain: "B" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Chain: "C" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2044 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 21, 'TRANS': 238} Chain breaks: 4 Chain: "D" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 2997 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Time building chain proxies: 5.66, per 1000 atoms: 0.56 Number of scatterers: 10082 At special positions: 0 Unit cell: (149.46, 121.9, 95.4, 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 16 16.00 O 1882 8.00 N 1814 7.00 C 6370 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: 3.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 14 sheets defined 28.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.605A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.888A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.939A pdb=" N LEU A 123 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 removed outlier: 3.799A pdb=" N LEU A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.636A pdb=" N LEU A 182 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.820A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 255 removed outlier: 3.565A pdb=" N ALA A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 removed outlier: 3.538A pdb=" N ALA A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.670A pdb=" N MET A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.548A pdb=" N ARG A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 removed outlier: 4.585A pdb=" N ILE B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 86 through 97 removed outlier: 4.193A pdb=" N ALA B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 97 " --> pdb=" O LYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.766A pdb=" N SER B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.604A pdb=" N ARG C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 82 removed outlier: 4.889A pdb=" N TRP C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.939A pdb=" N LEU C 123 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 removed outlier: 3.799A pdb=" N LEU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 178 through 187 removed outlier: 3.636A pdb=" N LEU C 182 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.819A pdb=" N ALA C 198 " --> pdb=" O ARG C 194 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 255 removed outlier: 3.566A pdb=" N ALA C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 248 " --> pdb=" O ARG C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.539A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 300 through 308 removed outlier: 3.671A pdb=" N MET C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.548A pdb=" N ARG C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 71 removed outlier: 4.585A pdb=" N ILE D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 86 through 97 removed outlier: 4.193A pdb=" N ALA D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE D 97 " --> pdb=" O LYS D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 458 removed outlier: 3.765A pdb=" N SER D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.341A pdb=" N LEU A 52 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 105 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.643A pdb=" N VAL B 158 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 141 " --> pdb=" O ASN B 156 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN B 172 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 159 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 189 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 191 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 197 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AA4, first strand: chain 'B' and resid 293 through 297 removed outlier: 4.031A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 396 through 397 removed outlier: 3.715A pdb=" N ARG B 426 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 419 removed outlier: 3.575A pdb=" N GLN B 419 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.341A pdb=" N LEU C 52 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 105 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 139 through 141 removed outlier: 3.642A pdb=" N VAL D 158 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER D 141 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN D 172 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL D 159 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 189 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 191 " --> pdb=" O LEU D 197 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D 197 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 206 through 210 Processing sheet with id=AB2, first strand: chain 'D' and resid 293 through 297 removed outlier: 4.031A pdb=" N LEU D 339 " --> pdb=" O ALA D 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 396 through 397 removed outlier: 3.714A pdb=" N ARG D 426 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 417 through 419 removed outlier: 3.576A pdb=" N GLN D 419 " --> pdb=" O GLY D 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 482 through 483 244 hydrogen bonds defined for protein. 672 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: 2.49 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3386 1.34 - 1.46: 1864 1.46 - 1.57: 5020 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 10298 Sorted by residual: bond pdb=" C PHE A 27 " pdb=" N PRO A 28 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.02e+00 bond pdb=" C PHE C 27 " pdb=" N PRO C 28 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.94e+00 bond pdb=" C SER D 255 " pdb=" N PRO D 256 " ideal model delta sigma weight residual 1.331 1.318 0.014 7.90e-03 1.60e+04 2.94e+00 bond pdb=" C SER B 255 " pdb=" N PRO B 256 " ideal model delta sigma weight residual 1.331 1.318 0.013 7.90e-03 1.60e+04 2.90e+00 bond pdb=" CA ALA B 182 " pdb=" C ALA B 182 " ideal model delta sigma weight residual 1.518 1.462 0.056 4.01e-02 6.22e+02 1.92e+00 ... (remaining 10293 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.73: 420 106.73 - 113.55: 5593 113.55 - 120.37: 3839 120.37 - 127.19: 3989 127.19 - 134.01: 143 Bond angle restraints: 13984 Sorted by residual: angle pdb=" N VAL D 258 " pdb=" CA VAL D 258 " pdb=" C VAL D 258 " ideal model delta sigma weight residual 112.98 108.27 4.71 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N VAL B 258 " pdb=" CA VAL B 258 " pdb=" C VAL B 258 " ideal model delta sigma weight residual 112.98 108.27 4.71 1.25e+00 6.40e-01 1.42e+01 angle pdb=" N GLU C 36 " pdb=" CA GLU C 36 " pdb=" C GLU C 36 " ideal model delta sigma weight residual 111.02 115.67 -4.65 1.25e+00 6.40e-01 1.38e+01 angle pdb=" N GLU A 36 " pdb=" CA GLU A 36 " pdb=" C GLU A 36 " ideal model delta sigma weight residual 111.02 115.64 -4.62 1.25e+00 6.40e-01 1.36e+01 angle pdb=" N VAL D 139 " pdb=" CA VAL D 139 " pdb=" C VAL D 139 " ideal model delta sigma weight residual 108.82 105.18 3.64 1.22e+00 6.72e-01 8.88e+00 ... (remaining 13979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5521 17.13 - 34.26: 524 34.26 - 51.39: 79 51.39 - 68.53: 14 68.53 - 85.66: 6 Dihedral angle restraints: 6144 sinusoidal: 2398 harmonic: 3746 Sorted by residual: dihedral pdb=" CA PRO C 34 " pdb=" C PRO C 34 " pdb=" N ASN C 35 " pdb=" CA ASN C 35 " ideal model delta harmonic sigma weight residual -180.00 -148.60 -31.40 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA PRO A 34 " pdb=" C PRO A 34 " pdb=" N ASN A 35 " pdb=" CA ASN A 35 " ideal model delta harmonic sigma weight residual -180.00 -148.62 -31.38 0 5.00e+00 4.00e-02 3.94e+01 dihedral pdb=" CA LEU C 101 " pdb=" C LEU C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta harmonic sigma weight residual -180.00 -150.26 -29.74 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1156 0.045 - 0.090: 310 0.090 - 0.135: 90 0.135 - 0.180: 12 0.180 - 0.225: 2 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CB THR A 92 " pdb=" CA THR A 92 " pdb=" OG1 THR A 92 " pdb=" CG2 THR A 92 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR C 92 " pdb=" CA THR C 92 " pdb=" OG1 THR C 92 " pdb=" CG2 THR C 92 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA VAL D 139 " pdb=" N VAL D 139 " pdb=" C VAL D 139 " pdb=" CB VAL D 139 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1567 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 478 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 479 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 479 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 478 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO B 479 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 189 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO B 190 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 190 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 190 " -0.025 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 644 2.71 - 3.26: 10480 3.26 - 3.81: 14724 3.81 - 4.35: 18561 4.35 - 4.90: 31280 Nonbonded interactions: 75689 Sorted by model distance: nonbonded pdb=" NE2 GLN B 419 " pdb=" OE1 GLU B 484 " model vdw 2.166 2.520 nonbonded pdb=" NE2 GLN D 419 " pdb=" OE1 GLU D 484 " model vdw 2.166 2.520 nonbonded pdb=" O VAL A 283 " pdb=" OG SER A 287 " model vdw 2.176 2.440 nonbonded pdb=" O VAL C 283 " pdb=" OG SER C 287 " model vdw 2.176 2.440 nonbonded pdb=" OG SER B 181 " pdb=" ND2 ASN B 184 " model vdw 2.187 2.520 ... (remaining 75684 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 'C' } ncs_group { reference = chain 'B' 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: 0.590 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: 2.430 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.080 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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: 34.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 0.056 10298 Z= 0.324 Angle : 0.804 6.441 13984 Z= 0.447 Chirality : 0.046 0.225 1570 Planarity : 0.005 0.057 1828 Dihedral : 13.701 85.657 3740 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % Rotamer: Outliers : 1.14 % Allowed : 4.36 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -6.35 (0.17), residues: 1288 helix: -3.60 (0.19), residues: 342 sheet: -4.96 (0.21), residues: 320 loop : -4.12 (0.19), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 244 HIS 0.003 0.001 HIS C 178 PHE 0.017 0.002 PHE B 396 TYR 0.014 0.001 TYR D 289 ARG 0.006 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: B 180 ARG cc_start: 0.6806 (ptp90) cc_final: 0.6391 (ptp90) REVERT: B 184 ASN cc_start: 0.7799 (m-40) cc_final: 0.6882 (t0) REVERT: B 283 MET cc_start: 0.8719 (mmt) cc_final: 0.8210 (mmt) REVERT: B 389 ASP cc_start: 0.8198 (t0) cc_final: 0.7925 (t0) REVERT: B 484 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7519 (mm-30) REVERT: C 43 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8649 (tp40) REVERT: D 180 ARG cc_start: 0.6930 (ptp90) cc_final: 0.6651 (ptp90) REVERT: D 184 ASN cc_start: 0.7863 (m-40) cc_final: 0.7085 (t0) REVERT: D 257 THR cc_start: 0.8739 (m) cc_final: 0.8428 (m) REVERT: D 283 MET cc_start: 0.8754 (mmt) cc_final: 0.7980 (mmt) REVERT: D 419 GLN cc_start: 0.6216 (tt0) cc_final: 0.5535 (tt0) REVERT: D 484 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7311 (mm-30) outliers start: 12 outliers final: 7 residues processed: 143 average time/residue: 0.2185 time to fit residues: 43.6090 Evaluate side-chains 101 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 354 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 215 HIS ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10298 Z= 0.209 Angle : 0.706 8.006 13984 Z= 0.351 Chirality : 0.044 0.156 1570 Planarity : 0.005 0.047 1828 Dihedral : 6.468 40.906 1451 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 0.95 % Allowed : 9.38 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -5.18 (0.20), residues: 1288 helix: -1.84 (0.26), residues: 342 sheet: -4.57 (0.22), residues: 298 loop : -3.80 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.003 0.001 HIS D 215 PHE 0.021 0.002 PHE D 100 TYR 0.012 0.001 TYR A 240 ARG 0.004 0.000 ARG D 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 184 ASN cc_start: 0.7764 (m110) cc_final: 0.6900 (t0) REVERT: B 209 GLN cc_start: 0.7879 (tp40) cc_final: 0.7425 (tp40) REVERT: B 216 GLU cc_start: 0.7758 (mt-10) cc_final: 0.6918 (mt-10) REVERT: B 283 MET cc_start: 0.8723 (mmt) cc_final: 0.8294 (mmt) REVERT: B 484 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7525 (mm-30) REVERT: B 486 ASN cc_start: 0.7314 (m-40) cc_final: 0.6569 (m-40) REVERT: D 180 ARG cc_start: 0.6878 (ptp90) cc_final: 0.6258 (mtp180) REVERT: D 184 ASN cc_start: 0.7727 (m110) cc_final: 0.7008 (t0) REVERT: D 283 MET cc_start: 0.8793 (mmt) cc_final: 0.8109 (mmt) outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 0.1924 time to fit residues: 31.8599 Evaluate side-chains 99 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 354 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 0.9980 chunk 129 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 96 optimal weight: 9.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 HIS ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10298 Z= 0.302 Angle : 0.715 8.063 13984 Z= 0.356 Chirality : 0.044 0.151 1570 Planarity : 0.005 0.045 1828 Dihedral : 6.515 34.439 1448 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % Rotamer: Outliers : 2.37 % Allowed : 11.74 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.66 (0.22), residues: 1288 helix: -1.10 (0.28), residues: 334 sheet: -4.45 (0.23), residues: 310 loop : -3.51 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.004 0.001 HIS B 215 PHE 0.022 0.002 PHE A 126 TYR 0.015 0.002 TYR B 289 ARG 0.003 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 0.903 Fit side-chains REVERT: B 180 ARG cc_start: 0.6790 (ptp90) cc_final: 0.6127 (ptp90) REVERT: B 184 ASN cc_start: 0.7909 (m110) cc_final: 0.7058 (t0) REVERT: B 209 GLN cc_start: 0.7935 (tp40) cc_final: 0.7670 (tp40) REVERT: B 216 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7112 (mt-10) REVERT: B 283 MET cc_start: 0.8693 (mmt) cc_final: 0.8183 (mmt) REVERT: B 484 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7244 (mm-30) REVERT: B 486 ASN cc_start: 0.7308 (m-40) cc_final: 0.5752 (m-40) REVERT: C 27 PHE cc_start: 0.6279 (t80) cc_final: 0.5981 (t80) REVERT: C 42 GLN cc_start: 0.8856 (tp40) cc_final: 0.8651 (tp40) REVERT: C 306 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7814 (mtmm) REVERT: D 184 ASN cc_start: 0.7764 (m110) cc_final: 0.7117 (t0) REVERT: D 283 MET cc_start: 0.8736 (mmt) cc_final: 0.7988 (mmt) outliers start: 25 outliers final: 17 residues processed: 119 average time/residue: 0.1682 time to fit residues: 30.6419 Evaluate side-chains 111 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 354 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS B 218 HIS C 76 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10298 Z= 0.368 Angle : 0.760 9.483 13984 Z= 0.377 Chirality : 0.045 0.155 1570 Planarity : 0.005 0.042 1828 Dihedral : 6.697 34.243 1448 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.93 % Favored : 81.91 % Rotamer: Outliers : 2.84 % Allowed : 14.58 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.48 (0.22), residues: 1288 helix: -0.83 (0.28), residues: 334 sheet: -4.45 (0.23), residues: 320 loop : -3.37 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS A 178 PHE 0.023 0.002 PHE D 100 TYR 0.018 0.002 TYR B 289 ARG 0.004 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 1.104 Fit side-chains REVERT: B 180 ARG cc_start: 0.6890 (ptp90) cc_final: 0.6150 (ptp90) REVERT: B 209 GLN cc_start: 0.7884 (tp40) cc_final: 0.7615 (tp40) REVERT: B 216 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7252 (mt-10) REVERT: B 283 MET cc_start: 0.8792 (mmt) cc_final: 0.7813 (mmt) REVERT: B 476 TYR cc_start: 0.8390 (t80) cc_final: 0.8164 (t80) REVERT: B 484 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7474 (mm-30) REVERT: B 486 ASN cc_start: 0.7309 (m-40) cc_final: 0.6418 (m-40) REVERT: C 27 PHE cc_start: 0.6377 (t80) cc_final: 0.6114 (t80) REVERT: D 184 ASN cc_start: 0.7869 (m110) cc_final: 0.7047 (t0) REVERT: D 283 MET cc_start: 0.8801 (mmt) cc_final: 0.7684 (mmt) outliers start: 30 outliers final: 25 residues processed: 125 average time/residue: 0.1771 time to fit residues: 34.0291 Evaluate side-chains 118 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 458 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10298 Z= 0.190 Angle : 0.684 9.382 13984 Z= 0.336 Chirality : 0.042 0.148 1570 Planarity : 0.004 0.039 1828 Dihedral : 6.129 34.059 1448 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.13 % Favored : 85.87 % Rotamer: Outliers : 2.18 % Allowed : 17.14 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.19 (0.22), residues: 1288 helix: -0.35 (0.29), residues: 332 sheet: -4.13 (0.25), residues: 306 loop : -3.47 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS C 202 PHE 0.014 0.001 PHE D 140 TYR 0.009 0.001 TYR A 186 ARG 0.002 0.000 ARG D 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8411 (mt) cc_final: 0.8113 (mp) REVERT: B 180 ARG cc_start: 0.6682 (ptp90) cc_final: 0.5935 (ptp90) REVERT: B 184 ASN cc_start: 0.7684 (m110) cc_final: 0.6844 (t0) REVERT: B 476 TYR cc_start: 0.8351 (t80) cc_final: 0.8125 (t80) REVERT: B 484 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 486 ASN cc_start: 0.7207 (m-40) cc_final: 0.6412 (m-40) REVERT: B 500 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6651 (ttt180) REVERT: C 27 PHE cc_start: 0.6320 (t80) cc_final: 0.6037 (t80) REVERT: D 209 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7954 (mm-40) outliers start: 23 outliers final: 12 residues processed: 113 average time/residue: 0.1753 time to fit residues: 30.2372 Evaluate side-chains 105 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 0.2980 chunk 10 optimal weight: 0.0060 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 0.8756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN B 64 GLN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10298 Z= 0.160 Angle : 0.654 9.651 13984 Z= 0.319 Chirality : 0.041 0.146 1570 Planarity : 0.004 0.038 1828 Dihedral : 5.683 33.807 1447 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 1.61 % Allowed : 17.90 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.91 (0.23), residues: 1288 helix: -0.01 (0.30), residues: 332 sheet: -3.92 (0.25), residues: 314 loop : -3.35 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.003 0.000 HIS A 202 PHE 0.024 0.002 PHE C 126 TYR 0.008 0.001 TYR C 240 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8542 (tp40) cc_final: 0.7668 (tm-30) REVERT: B 180 ARG cc_start: 0.6556 (ptp90) cc_final: 0.5910 (ptp90) REVERT: B 184 ASN cc_start: 0.7570 (m110) cc_final: 0.6698 (t0) REVERT: B 476 TYR cc_start: 0.8266 (t80) cc_final: 0.8017 (t80) REVERT: B 484 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7603 (mm-30) REVERT: B 486 ASN cc_start: 0.7121 (m-40) cc_final: 0.6266 (m-40) REVERT: C 27 PHE cc_start: 0.6467 (t80) cc_final: 0.6088 (t80) REVERT: C 282 MET cc_start: 0.8193 (mtt) cc_final: 0.7845 (mtp) REVERT: D 209 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8058 (mm110) REVERT: D 476 TYR cc_start: 0.8253 (t80) cc_final: 0.7956 (t80) REVERT: D 500 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6455 (ttt180) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 0.2022 time to fit residues: 33.7200 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 500 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 40.0000 chunk 107 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10298 Z= 0.421 Angle : 0.803 9.568 13984 Z= 0.397 Chirality : 0.046 0.182 1570 Planarity : 0.005 0.039 1828 Dihedral : 6.406 33.513 1444 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.94 % Favored : 80.90 % Rotamer: Outliers : 2.75 % Allowed : 18.09 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.10 (0.23), residues: 1288 helix: -0.18 (0.29), residues: 332 sheet: -4.27 (0.24), residues: 328 loop : -3.27 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 168 HIS 0.005 0.001 HIS C 202 PHE 0.020 0.003 PHE B 140 TYR 0.017 0.002 TYR B 289 ARG 0.004 0.000 ARG D 279 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.013 Fit side-chains REVERT: B 283 MET cc_start: 0.8770 (mmt) cc_final: 0.7727 (mmt) REVERT: B 306 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8535 (p0) REVERT: B 419 GLN cc_start: 0.6478 (tt0) cc_final: 0.5702 (tt0) REVERT: B 484 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 500 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6677 (ttt180) REVERT: C 27 PHE cc_start: 0.6472 (t80) cc_final: 0.6205 (t80) REVERT: C 306 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7848 (mtmm) REVERT: D 209 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8019 (mm110) REVERT: D 283 MET cc_start: 0.8773 (mmt) cc_final: 0.7557 (mmt) REVERT: D 500 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6563 (ttt180) outliers start: 29 outliers final: 19 residues processed: 116 average time/residue: 0.1861 time to fit residues: 31.9737 Evaluate side-chains 111 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain C residue 310 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 500 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.0170 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 100 optimal weight: 0.0670 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10298 Z= 0.169 Angle : 0.682 9.764 13984 Z= 0.337 Chirality : 0.042 0.174 1570 Planarity : 0.004 0.040 1828 Dihedral : 5.787 33.379 1444 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 1.33 % Allowed : 19.70 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.81 (0.23), residues: 1288 helix: 0.18 (0.30), residues: 330 sheet: -3.96 (0.24), residues: 314 loop : -3.29 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 168 HIS 0.003 0.001 HIS A 202 PHE 0.025 0.002 PHE B 100 TYR 0.009 0.001 TYR A 186 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8423 (tp40) cc_final: 0.7617 (tm-30) REVERT: B 209 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8084 (mm-40) REVERT: B 484 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 500 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6554 (ttt180) REVERT: C 27 PHE cc_start: 0.6351 (t80) cc_final: 0.6053 (t80) REVERT: C 306 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7811 (mtmm) REVERT: D 500 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6402 (ttt180) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 0.1933 time to fit residues: 29.5332 Evaluate side-chains 98 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 500 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10298 Z= 0.310 Angle : 0.737 10.086 13984 Z= 0.362 Chirality : 0.044 0.156 1570 Planarity : 0.004 0.038 1828 Dihedral : 6.060 33.116 1444 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.40 % Favored : 81.44 % Rotamer: Outliers : 1.80 % Allowed : 19.13 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.94 (0.23), residues: 1288 helix: 0.09 (0.30), residues: 330 sheet: -4.14 (0.23), residues: 328 loop : -3.28 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.003 0.001 HIS C 178 PHE 0.021 0.002 PHE D 140 TYR 0.018 0.002 TYR D 476 ARG 0.003 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.070 Fit side-chains REVERT: A 211 GLN cc_start: 0.8522 (tp40) cc_final: 0.7596 (tm-30) REVERT: B 283 MET cc_start: 0.8748 (mmt) cc_final: 0.7677 (mmt) REVERT: B 484 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7316 (mm-30) REVERT: B 500 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6571 (ttt180) REVERT: C 27 PHE cc_start: 0.6526 (t80) cc_final: 0.6257 (t80) REVERT: C 306 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7821 (mtmm) REVERT: D 216 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7547 (mt-10) REVERT: D 283 MET cc_start: 0.8751 (mmt) cc_final: 0.7541 (mmt) REVERT: D 500 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6487 (ttt180) outliers start: 19 outliers final: 17 residues processed: 106 average time/residue: 0.1890 time to fit residues: 30.0238 Evaluate side-chains 107 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 500 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10298 Z= 0.253 Angle : 0.705 10.048 13984 Z= 0.346 Chirality : 0.043 0.159 1570 Planarity : 0.004 0.038 1828 Dihedral : 5.981 33.111 1444 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.13 % Favored : 85.87 % Rotamer: Outliers : 1.89 % Allowed : 19.32 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.87 (0.23), residues: 1288 helix: 0.14 (0.30), residues: 330 sheet: -4.02 (0.24), residues: 326 loop : -3.27 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.003 0.001 HIS C 202 PHE 0.030 0.002 PHE D 100 TYR 0.019 0.001 TYR D 476 ARG 0.002 0.000 ARG B 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLN cc_start: 0.8445 (tp40) cc_final: 0.7624 (tm-30) REVERT: B 484 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 500 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6556 (ttt180) REVERT: C 27 PHE cc_start: 0.6326 (t80) cc_final: 0.6074 (t80) REVERT: C 306 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7801 (mtmm) REVERT: D 500 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6462 (ttt180) outliers start: 20 outliers final: 18 residues processed: 108 average time/residue: 0.1976 time to fit residues: 31.8989 Evaluate side-chains 111 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 91 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 500 ARG Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 446 ASP Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 500 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 29 optimal weight: 0.0060 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 1.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.145342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128760 restraints weight = 15663.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129437 restraints weight = 29259.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129750 restraints weight = 20771.036| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10298 Z= 0.189 Angle : 0.675 9.887 13984 Z= 0.329 Chirality : 0.042 0.155 1570 Planarity : 0.004 0.039 1828 Dihedral : 5.631 32.912 1444 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.45 % Favored : 84.55 % Rotamer: Outliers : 1.52 % Allowed : 19.70 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.72 (0.23), residues: 1288 helix: 0.26 (0.30), residues: 330 sheet: -3.80 (0.25), residues: 316 loop : -3.30 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.002 0.001 HIS A 202 PHE 0.018 0.001 PHE C 126 TYR 0.018 0.001 TYR D 476 ARG 0.002 0.000 ARG B 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.70 seconds wall clock time: 32 minutes 14.77 seconds (1934.77 seconds total)