Starting phenix.real_space_refine on Sat Dec 28 06:17:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tyw_41729/12_2024/8tyw_41729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tyw_41729/12_2024/8tyw_41729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tyw_41729/12_2024/8tyw_41729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tyw_41729/12_2024/8tyw_41729.map" model { file = "/net/cci-nas-00/data/ceres_data/8tyw_41729/12_2024/8tyw_41729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tyw_41729/12_2024/8tyw_41729.cif" } resolution = 3.43 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= 0.026 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 47 5.16 5 C 5022 2.51 5 N 1386 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7938 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2012 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1938 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 437 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 958 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.72, per 1000 atoms: 0.59 Number of scatterers: 7938 At special positions: 0 Unit cell: (75.712, 104.832, 128.96, 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 47 16.00 O 1483 8.00 N 1386 7.00 C 5022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 209 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 41.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.807A pdb=" N VAL A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 135 removed outlier: 3.861A pdb=" N TYR A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 172 Processing helix chain 'A' and resid 173 through 176 removed outlier: 3.541A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 178 through 206 removed outlier: 4.477A pdb=" N GLY A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.520A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 263 removed outlier: 3.995A pdb=" N VAL A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 302 removed outlier: 4.591A pdb=" N THR A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 307 through 330 removed outlier: 4.314A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Proline residue: A 317 - end of helix Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 333 through 344 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.654A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.645A pdb=" N GLN B 32 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 39 removed outlier: 3.939A pdb=" N GLN C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 64 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.548A pdb=" N CYS C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 removed outlier: 4.032A pdb=" N ALA C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.524A pdb=" N GLU C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 Proline residue: C 313 - end of helix removed outlier: 3.662A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 353 removed outlier: 3.892A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.629A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.539A pdb=" N ASP N 90 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 52 removed outlier: 4.083A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.669A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.464A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.561A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.657A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.742A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.969A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 214 removed outlier: 3.920A pdb=" N ASP C 223 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR C 210 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET C 221 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N HIS C 41 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE C 222 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 43 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL C 224 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LEU C 45 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG C 42 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE C 245 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 46 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA C 249 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.932A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.601A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1164 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: 2.24 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2601 1.34 - 1.46: 1430 1.46 - 1.57: 4000 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 8096 Sorted by residual: bond pdb=" CA THR B 50 " pdb=" CB THR B 50 " ideal model delta sigma weight residual 1.528 1.569 -0.041 1.51e-02 4.39e+03 7.35e+00 bond pdb=" CG LEU C 346 " pdb=" CD2 LEU C 346 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.24e+00 bond pdb=" CB LYS C 271 " pdb=" CG LYS C 271 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CD LYS C 271 " pdb=" CE LYS C 271 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB ASN A 321 " pdb=" CG ASN A 321 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.37e+00 ... (remaining 8091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 10733 2.67 - 5.33: 209 5.33 - 8.00: 41 8.00 - 10.67: 12 10.67 - 13.34: 2 Bond angle restraints: 10997 Sorted by residual: angle pdb=" CB LYS C 271 " pdb=" CG LYS C 271 " pdb=" CD LYS C 271 " ideal model delta sigma weight residual 111.30 97.96 13.34 2.30e+00 1.89e-01 3.36e+01 angle pdb=" CB ARG A 179 " pdb=" CG ARG A 179 " pdb=" CD ARG A 179 " ideal model delta sigma weight residual 111.30 121.33 -10.03 2.30e+00 1.89e-01 1.90e+01 angle pdb=" CA ILE A 86 " pdb=" CB ILE A 86 " pdb=" CG1 ILE A 86 " ideal model delta sigma weight residual 110.40 117.81 -7.41 1.70e+00 3.46e-01 1.90e+01 angle pdb=" CA GLU G 22 " pdb=" CB GLU G 22 " pdb=" CG GLU G 22 " ideal model delta sigma weight residual 114.10 122.81 -8.71 2.00e+00 2.50e-01 1.90e+01 angle pdb=" CG ARG G 13 " pdb=" CD ARG G 13 " pdb=" NE ARG G 13 " ideal model delta sigma weight residual 112.00 121.27 -9.27 2.20e+00 2.07e-01 1.78e+01 ... (remaining 10992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 4024 17.37 - 34.74: 558 34.74 - 52.11: 175 52.11 - 69.48: 34 69.48 - 86.85: 12 Dihedral angle restraints: 4803 sinusoidal: 1827 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 157.76 -64.76 1 1.00e+01 1.00e-02 5.51e+01 dihedral pdb=" CA ASN A 172 " pdb=" C ASN A 172 " pdb=" N ALA A 173 " pdb=" CA ALA A 173 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLN A 132 " pdb=" C GLN A 132 " pdb=" N TYR A 133 " pdb=" CA TYR A 133 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 4800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1069 0.072 - 0.144: 173 0.144 - 0.217: 18 0.217 - 0.289: 2 0.289 - 0.361: 3 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CB VAL A 283 " pdb=" CA VAL A 283 " pdb=" CG1 VAL A 283 " pdb=" CG2 VAL A 283 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB THR A 192 " pdb=" CA THR A 192 " pdb=" OG1 THR A 192 " pdb=" CG2 THR A 192 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CG LEU A 281 " pdb=" CB LEU A 281 " pdb=" CD1 LEU A 281 " pdb=" CD2 LEU A 281 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1262 not shown) Planarity restraints: 1405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 362 " 0.023 2.00e-02 2.50e+03 2.41e-02 8.72e+00 pdb=" CG HIS C 362 " -0.051 2.00e-02 2.50e+03 pdb=" ND1 HIS C 362 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS C 362 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 HIS C 362 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS C 362 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 105 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.16e+00 pdb=" N PRO A 106 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 68 " 0.190 9.50e-02 1.11e+02 8.57e-02 5.60e+00 pdb=" NE ARG B 68 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 68 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG B 68 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 68 " 0.001 2.00e-02 2.50e+03 ... (remaining 1402 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2448 2.82 - 3.34: 7113 3.34 - 3.86: 13388 3.86 - 4.38: 14455 4.38 - 4.90: 25591 Nonbonded interactions: 62995 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 2.309 3.040 nonbonded pdb=" OG SER N 112 " pdb=" O THR N 114 " model vdw 2.319 3.040 nonbonded pdb=" NZ LYS B 78 " pdb=" OD2 ASP C 33 " model vdw 2.331 3.120 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.337 3.040 ... (remaining 62990 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.040 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 0.068 8096 Z= 0.321 Angle : 0.931 13.336 10997 Z= 0.484 Chirality : 0.055 0.361 1265 Planarity : 0.007 0.086 1405 Dihedral : 18.203 86.850 2870 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.59 % Allowed : 37.75 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.15 (0.24), residues: 1008 helix: -0.24 (0.22), residues: 401 sheet: -0.09 (0.38), residues: 207 loop : -1.57 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 234 HIS 0.025 0.002 HIS C 362 PHE 0.029 0.002 PHE C 212 TYR 0.011 0.002 TYR B 289 ARG 0.022 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 274 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8423 (m-10) cc_final: 0.8132 (m-80) REVERT: A 179 ARG cc_start: 0.7767 (tpp-160) cc_final: 0.7479 (tpp-160) REVERT: A 281 LEU cc_start: 0.8104 (tp) cc_final: 0.7788 (mm) REVERT: B 22 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8046 (ttm-80) REVERT: B 258 ASP cc_start: 0.7576 (t0) cc_final: 0.7163 (t0) REVERT: B 278 PHE cc_start: 0.8697 (m-80) cc_final: 0.8279 (m-80) REVERT: C 273 PHE cc_start: 0.8151 (t80) cc_final: 0.7806 (t80) REVERT: G 13 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7720 (ptt-90) outliers start: 5 outliers final: 2 residues processed: 275 average time/residue: 0.2844 time to fit residues: 96.6285 Evaluate side-chains 271 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain C residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 ASN C 267 GLN C 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8096 Z= 0.197 Angle : 0.561 6.858 10997 Z= 0.297 Chirality : 0.042 0.159 1265 Planarity : 0.004 0.061 1405 Dihedral : 4.532 39.541 1116 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.21 % Allowed : 31.72 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1008 helix: 1.37 (0.25), residues: 398 sheet: 0.04 (0.37), residues: 212 loop : -1.38 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 234 HIS 0.003 0.001 HIS A 128 PHE 0.009 0.001 PHE C 363 TYR 0.009 0.001 TYR N 95 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7441 (tpp-160) REVERT: A 246 VAL cc_start: 0.8511 (t) cc_final: 0.8232 (p) REVERT: B 22 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8168 (ttm-80) REVERT: B 136 SER cc_start: 0.8525 (p) cc_final: 0.8168 (m) REVERT: B 142 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.6150 (p90) REVERT: B 186 ASP cc_start: 0.7790 (p0) cc_final: 0.7575 (p0) REVERT: B 219 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7614 (mmt90) REVERT: B 261 LEU cc_start: 0.8449 (mt) cc_final: 0.8231 (mp) REVERT: B 294 CYS cc_start: 0.8338 (p) cc_final: 0.8067 (p) REVERT: B 298 ASP cc_start: 0.7673 (t70) cc_final: 0.7209 (t0) REVERT: B 331 SER cc_start: 0.8385 (t) cc_final: 0.8092 (p) REVERT: C 12 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: C 210 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7760 (p) REVERT: C 230 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7346 (mt-10) REVERT: C 233 LYS cc_start: 0.8369 (mtpp) cc_final: 0.8123 (mtpp) REVERT: C 273 PHE cc_start: 0.8264 (t80) cc_final: 0.7955 (t80) REVERT: G 14 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (pttm) outliers start: 44 outliers final: 23 residues processed: 306 average time/residue: 0.2657 time to fit residues: 101.7831 Evaluate side-chains 302 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.0040 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 0.0010 chunk 90 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8096 Z= 0.152 Angle : 0.538 7.580 10997 Z= 0.278 Chirality : 0.042 0.161 1265 Planarity : 0.003 0.055 1405 Dihedral : 4.223 36.826 1114 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.56 % Allowed : 31.83 % Favored : 62.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1008 helix: 1.86 (0.25), residues: 402 sheet: 0.13 (0.36), residues: 216 loop : -1.33 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 234 HIS 0.002 0.001 HIS B 54 PHE 0.006 0.001 PHE B 278 TYR 0.009 0.001 TYR N 95 ARG 0.008 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 SER cc_start: 0.8591 (m) cc_final: 0.8206 (p) REVERT: A 179 ARG cc_start: 0.7778 (tpp-160) cc_final: 0.7347 (tpp-160) REVERT: A 183 LEU cc_start: 0.8471 (tt) cc_final: 0.8015 (tt) REVERT: A 246 VAL cc_start: 0.8472 (t) cc_final: 0.8214 (p) REVERT: B 17 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8239 (tp-100) REVERT: B 22 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.7788 (mtm-85) REVERT: B 118 ASP cc_start: 0.7777 (p0) cc_final: 0.7555 (p0) REVERT: B 136 SER cc_start: 0.8493 (p) cc_final: 0.8115 (m) REVERT: B 142 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6097 (p90) REVERT: B 256 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7639 (mtt-85) REVERT: B 258 ASP cc_start: 0.7783 (t0) cc_final: 0.7175 (t0) REVERT: B 261 LEU cc_start: 0.8380 (mt) cc_final: 0.8179 (mp) REVERT: B 294 CYS cc_start: 0.8342 (p) cc_final: 0.8055 (p) REVERT: B 298 ASP cc_start: 0.7692 (t70) cc_final: 0.7168 (t0) REVERT: B 331 SER cc_start: 0.8381 (t) cc_final: 0.8012 (p) REVERT: C 12 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: C 210 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7630 (p) REVERT: C 273 PHE cc_start: 0.8248 (t80) cc_final: 0.7996 (t80) REVERT: G 14 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8689 (pttm) outliers start: 47 outliers final: 28 residues processed: 287 average time/residue: 0.2750 time to fit residues: 98.9512 Evaluate side-chains 295 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8096 Z= 0.216 Angle : 0.549 7.415 10997 Z= 0.285 Chirality : 0.043 0.179 1265 Planarity : 0.003 0.051 1405 Dihedral : 4.075 18.249 1112 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.56 % Allowed : 32.43 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1008 helix: 1.82 (0.26), residues: 415 sheet: 0.03 (0.35), residues: 219 loop : -1.22 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 234 HIS 0.004 0.001 HIS C 362 PHE 0.009 0.001 PHE C 222 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6645 (t0) REVERT: A 157 SER cc_start: 0.8618 (m) cc_final: 0.8213 (p) REVERT: A 179 ARG cc_start: 0.7753 (tpp-160) cc_final: 0.7464 (tpp-160) REVERT: A 183 LEU cc_start: 0.8529 (tt) cc_final: 0.8162 (tt) REVERT: A 246 VAL cc_start: 0.8493 (t) cc_final: 0.8261 (p) REVERT: B 3 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: B 17 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8240 (tp-100) REVERT: B 22 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.7985 (ttm-80) REVERT: B 33 ILE cc_start: 0.9017 (tt) cc_final: 0.8719 (mp) REVERT: B 100 VAL cc_start: 0.8452 (m) cc_final: 0.8082 (p) REVERT: B 136 SER cc_start: 0.8547 (p) cc_final: 0.8125 (m) REVERT: B 142 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6134 (p90) REVERT: B 219 ARG cc_start: 0.7945 (mmt90) cc_final: 0.7530 (mmt90) REVERT: B 258 ASP cc_start: 0.7833 (t0) cc_final: 0.7255 (t0) REVERT: B 261 LEU cc_start: 0.8374 (mt) cc_final: 0.8159 (mp) REVERT: B 278 PHE cc_start: 0.8831 (m-80) cc_final: 0.8271 (m-80) REVERT: B 294 CYS cc_start: 0.8356 (p) cc_final: 0.8028 (p) REVERT: B 298 ASP cc_start: 0.7711 (t70) cc_final: 0.7122 (t0) REVERT: C 12 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: C 211 LYS cc_start: 0.8376 (mmmm) cc_final: 0.7932 (mmmm) REVERT: C 222 PHE cc_start: 0.8117 (m-80) cc_final: 0.7899 (m-80) REVERT: C 273 PHE cc_start: 0.8312 (t80) cc_final: 0.8007 (t80) REVERT: C 299 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: C 392 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7043 (mm-30) REVERT: G 14 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8668 (pttm) REVERT: N 72 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7168 (ttm-80) REVERT: N 91 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8441 (t) outliers start: 47 outliers final: 31 residues processed: 303 average time/residue: 0.2603 time to fit residues: 99.0687 Evaluate side-chains 312 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN B 125 ASN C 220 HIS ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8096 Z= 0.186 Angle : 0.543 7.629 10997 Z= 0.282 Chirality : 0.043 0.218 1265 Planarity : 0.003 0.050 1405 Dihedral : 4.010 18.383 1112 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 7.10 % Allowed : 31.60 % Favored : 61.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 1008 helix: 1.97 (0.26), residues: 409 sheet: 0.04 (0.35), residues: 219 loop : -1.06 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.013 0.001 HIS C 362 PHE 0.007 0.001 PHE B 253 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 278 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6635 (t0) REVERT: A 157 SER cc_start: 0.8607 (m) cc_final: 0.8181 (p) REVERT: A 179 ARG cc_start: 0.7741 (tpp-160) cc_final: 0.7475 (tpp-160) REVERT: A 246 VAL cc_start: 0.8484 (t) cc_final: 0.8251 (p) REVERT: B 3 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: B 17 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8232 (tp-100) REVERT: B 22 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.7889 (ttm-80) REVERT: B 33 ILE cc_start: 0.9041 (tt) cc_final: 0.8756 (mp) REVERT: B 100 VAL cc_start: 0.8524 (m) cc_final: 0.8168 (p) REVERT: B 118 ASP cc_start: 0.7794 (p0) cc_final: 0.7455 (p0) REVERT: B 136 SER cc_start: 0.8482 (p) cc_final: 0.8068 (m) REVERT: B 142 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.6189 (p90) REVERT: B 212 ASP cc_start: 0.7355 (p0) cc_final: 0.6865 (p0) REVERT: B 219 ARG cc_start: 0.7950 (mmt90) cc_final: 0.7689 (mmt90) REVERT: B 230 ASN cc_start: 0.8574 (m-40) cc_final: 0.8206 (m-40) REVERT: B 256 ARG cc_start: 0.7917 (mtt90) cc_final: 0.7612 (mtt90) REVERT: B 258 ASP cc_start: 0.7839 (t0) cc_final: 0.7247 (t0) REVERT: B 261 LEU cc_start: 0.8373 (mt) cc_final: 0.8162 (mp) REVERT: B 294 CYS cc_start: 0.8330 (p) cc_final: 0.7935 (p) REVERT: B 298 ASP cc_start: 0.7750 (t70) cc_final: 0.7137 (t0) REVERT: B 301 LYS cc_start: 0.8023 (ptpt) cc_final: 0.7694 (ptpt) REVERT: B 331 SER cc_start: 0.8382 (t) cc_final: 0.8083 (p) REVERT: C 12 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: C 211 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7821 (mmmm) REVERT: C 271 LYS cc_start: 0.8512 (mmtp) cc_final: 0.8220 (mmtp) REVERT: C 273 PHE cc_start: 0.8317 (t80) cc_final: 0.8016 (t80) REVERT: C 299 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: C 392 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7026 (mm-30) REVERT: G 14 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8652 (pttm) REVERT: N 72 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.6979 (ttm-80) REVERT: N 91 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8462 (t) outliers start: 60 outliers final: 38 residues processed: 316 average time/residue: 0.2623 time to fit residues: 104.1645 Evaluate side-chains 322 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8096 Z= 0.183 Angle : 0.549 7.312 10997 Z= 0.287 Chirality : 0.043 0.191 1265 Planarity : 0.003 0.049 1405 Dihedral : 3.963 18.116 1112 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 6.86 % Allowed : 32.54 % Favored : 60.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1008 helix: 2.00 (0.26), residues: 408 sheet: 0.15 (0.36), residues: 214 loop : -1.01 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 234 HIS 0.011 0.001 HIS C 362 PHE 0.009 0.001 PHE C 219 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 277 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.6608 (t0) REVERT: A 157 SER cc_start: 0.8603 (m) cc_final: 0.8172 (p) REVERT: A 179 ARG cc_start: 0.7749 (tpp-160) cc_final: 0.7471 (tpp-160) REVERT: A 246 VAL cc_start: 0.8486 (t) cc_final: 0.8252 (p) REVERT: B 3 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7630 (tp30) REVERT: B 22 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.7598 (mtm-85) REVERT: B 33 ILE cc_start: 0.9046 (tt) cc_final: 0.8774 (mp) REVERT: B 100 VAL cc_start: 0.8507 (m) cc_final: 0.8174 (p) REVERT: B 136 SER cc_start: 0.8496 (p) cc_final: 0.8092 (m) REVERT: B 142 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.6178 (p90) REVERT: B 204 CYS cc_start: 0.8148 (m) cc_final: 0.7851 (m) REVERT: B 256 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7664 (mtt90) REVERT: B 258 ASP cc_start: 0.7859 (t0) cc_final: 0.7161 (t0) REVERT: B 261 LEU cc_start: 0.8377 (mt) cc_final: 0.8165 (mp) REVERT: B 294 CYS cc_start: 0.8346 (p) cc_final: 0.7941 (p) REVERT: B 298 ASP cc_start: 0.7740 (t70) cc_final: 0.7090 (t0) REVERT: B 301 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7671 (ptpt) REVERT: B 331 SER cc_start: 0.8383 (t) cc_final: 0.8136 (t) REVERT: C 12 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: C 273 PHE cc_start: 0.8295 (t80) cc_final: 0.7727 (t80) REVERT: C 299 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6182 (mp0) REVERT: C 392 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7005 (mm-30) REVERT: G 14 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8635 (pttm) REVERT: N 72 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6920 (ttm-80) REVERT: N 91 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8458 (t) outliers start: 58 outliers final: 39 residues processed: 313 average time/residue: 0.2538 time to fit residues: 99.7394 Evaluate side-chains 323 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 276 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 216 LYS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8096 Z= 0.191 Angle : 0.564 7.073 10997 Z= 0.293 Chirality : 0.043 0.197 1265 Planarity : 0.003 0.049 1405 Dihedral : 4.000 21.513 1112 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 7.10 % Allowed : 32.31 % Favored : 60.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 1008 helix: 2.01 (0.26), residues: 408 sheet: 0.23 (0.36), residues: 213 loop : -0.98 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.011 0.001 HIS C 362 PHE 0.007 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.016 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6639 (t0) REVERT: A 119 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7159 (tp) REVERT: A 157 SER cc_start: 0.8610 (m) cc_final: 0.8177 (p) REVERT: A 179 ARG cc_start: 0.7750 (tpp-160) cc_final: 0.7432 (tpp-160) REVERT: A 183 LEU cc_start: 0.8688 (tt) cc_final: 0.8297 (tp) REVERT: A 246 VAL cc_start: 0.8484 (t) cc_final: 0.8252 (p) REVERT: B 3 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: B 22 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.7890 (ttm-80) REVERT: B 33 ILE cc_start: 0.9048 (tt) cc_final: 0.8793 (mp) REVERT: B 57 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8210 (ptpp) REVERT: B 100 VAL cc_start: 0.8533 (m) cc_final: 0.8236 (p) REVERT: B 118 ASP cc_start: 0.7775 (p0) cc_final: 0.7446 (p0) REVERT: B 136 SER cc_start: 0.8497 (p) cc_final: 0.8106 (m) REVERT: B 142 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.6130 (p90) REVERT: B 161 SER cc_start: 0.8215 (m) cc_final: 0.7596 (p) REVERT: B 175 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7699 (mm-40) REVERT: B 219 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7669 (mmt90) REVERT: B 230 ASN cc_start: 0.8564 (m-40) cc_final: 0.8247 (m-40) REVERT: B 256 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7554 (mtt90) REVERT: B 258 ASP cc_start: 0.7871 (t0) cc_final: 0.7279 (t0) REVERT: B 261 LEU cc_start: 0.8375 (mt) cc_final: 0.8157 (mp) REVERT: B 298 ASP cc_start: 0.7672 (t70) cc_final: 0.7073 (t0) REVERT: B 331 SER cc_start: 0.8315 (t) cc_final: 0.8080 (p) REVERT: C 12 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7686 (pm20) REVERT: C 271 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8189 (mmtp) REVERT: C 273 PHE cc_start: 0.8304 (t80) cc_final: 0.8050 (t80) REVERT: C 299 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: C 392 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7006 (mm-30) REVERT: G 14 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8586 (pttm) REVERT: G 47 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: N 72 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6884 (ttm-80) outliers start: 60 outliers final: 43 residues processed: 315 average time/residue: 0.2694 time to fit residues: 106.6700 Evaluate side-chains 329 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8096 Z= 0.233 Angle : 0.585 7.184 10997 Z= 0.306 Chirality : 0.044 0.206 1265 Planarity : 0.003 0.048 1405 Dihedral : 4.070 19.259 1112 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 6.51 % Allowed : 33.61 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1008 helix: 2.03 (0.26), residues: 404 sheet: 0.09 (0.35), residues: 223 loop : -0.87 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 234 HIS 0.011 0.001 HIS C 362 PHE 0.020 0.001 PHE B 199 TYR 0.013 0.001 TYR N 95 ARG 0.013 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 283 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6652 (t0) REVERT: A 119 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7168 (tp) REVERT: A 157 SER cc_start: 0.8648 (m) cc_final: 0.8213 (p) REVERT: A 179 ARG cc_start: 0.7747 (tpp-160) cc_final: 0.7444 (tpp-160) REVERT: A 183 LEU cc_start: 0.8730 (tt) cc_final: 0.8338 (tp) REVERT: A 246 VAL cc_start: 0.8504 (t) cc_final: 0.8266 (p) REVERT: B 22 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.7504 (ttm-80) REVERT: B 33 ILE cc_start: 0.9071 (tt) cc_final: 0.8823 (mp) REVERT: B 52 ARG cc_start: 0.7242 (mtm180) cc_final: 0.6890 (mtm180) REVERT: B 57 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8223 (ptpp) REVERT: B 100 VAL cc_start: 0.8548 (m) cc_final: 0.8304 (p) REVERT: B 118 ASP cc_start: 0.7795 (p0) cc_final: 0.7547 (p0) REVERT: B 136 SER cc_start: 0.8511 (p) cc_final: 0.8121 (m) REVERT: B 142 HIS cc_start: 0.6837 (OUTLIER) cc_final: 0.6154 (p90) REVERT: B 161 SER cc_start: 0.8366 (m) cc_final: 0.7869 (p) REVERT: B 175 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7647 (mm-40) REVERT: B 230 ASN cc_start: 0.8542 (m-40) cc_final: 0.8219 (m-40) REVERT: B 258 ASP cc_start: 0.7854 (t0) cc_final: 0.6994 (t0) REVERT: B 283 ARG cc_start: 0.8270 (tpt-90) cc_final: 0.7746 (tpt-90) REVERT: B 298 ASP cc_start: 0.7671 (t70) cc_final: 0.6788 (t0) REVERT: C 12 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: C 271 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8276 (mmtp) REVERT: C 273 PHE cc_start: 0.8321 (t80) cc_final: 0.7753 (t80) REVERT: C 392 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6975 (mm-30) REVERT: G 13 ARG cc_start: 0.8223 (mtm110) cc_final: 0.7695 (ptt-90) REVERT: G 14 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8639 (pttm) REVERT: N 72 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6910 (ttm-80) outliers start: 55 outliers final: 46 residues processed: 318 average time/residue: 0.2720 time to fit residues: 108.2215 Evaluate side-chains 334 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8096 Z= 0.238 Angle : 0.597 7.340 10997 Z= 0.312 Chirality : 0.044 0.214 1265 Planarity : 0.003 0.047 1405 Dihedral : 4.138 19.357 1112 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 7.10 % Allowed : 33.49 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1008 helix: 1.95 (0.26), residues: 411 sheet: 0.10 (0.35), residues: 220 loop : -0.92 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 234 HIS 0.010 0.001 HIS C 362 PHE 0.020 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.013 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6624 (t0) REVERT: A 119 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7180 (tp) REVERT: A 157 SER cc_start: 0.8660 (m) cc_final: 0.8228 (p) REVERT: A 164 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8811 (t) REVERT: A 179 ARG cc_start: 0.7766 (tpp-160) cc_final: 0.7452 (tpp-160) REVERT: A 183 LEU cc_start: 0.8772 (tt) cc_final: 0.8316 (tp) REVERT: A 246 VAL cc_start: 0.8497 (t) cc_final: 0.8259 (p) REVERT: B 22 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.7555 (ttm-80) REVERT: B 33 ILE cc_start: 0.9067 (tt) cc_final: 0.8848 (mp) REVERT: B 52 ARG cc_start: 0.7276 (mtm180) cc_final: 0.6965 (mtm180) REVERT: B 57 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8227 (ptpp) REVERT: B 118 ASP cc_start: 0.7803 (p0) cc_final: 0.7535 (p0) REVERT: B 136 SER cc_start: 0.8507 (p) cc_final: 0.8118 (m) REVERT: B 142 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6334 (p90) REVERT: B 161 SER cc_start: 0.8438 (m) cc_final: 0.7991 (p) REVERT: B 175 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7656 (mm-40) REVERT: B 217 MET cc_start: 0.7863 (mtt) cc_final: 0.7590 (mtt) REVERT: B 219 ARG cc_start: 0.7901 (mmt90) cc_final: 0.7521 (mpt-90) REVERT: B 258 ASP cc_start: 0.7873 (t0) cc_final: 0.6981 (t0) REVERT: B 283 ARG cc_start: 0.8262 (tpt-90) cc_final: 0.7703 (tpt-90) REVERT: B 298 ASP cc_start: 0.7699 (t70) cc_final: 0.6787 (t0) REVERT: C 232 ARG cc_start: 0.8755 (ttp-110) cc_final: 0.8510 (ttp-110) REVERT: C 271 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8271 (mmtp) REVERT: C 273 PHE cc_start: 0.8342 (t80) cc_final: 0.7767 (t80) REVERT: C 299 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6225 (mp0) REVERT: C 374 ARG cc_start: 0.8396 (ttp-170) cc_final: 0.8158 (ttp-170) REVERT: C 392 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6997 (mm-30) REVERT: G 13 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7902 (mtm110) REVERT: G 14 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8632 (pttm) REVERT: G 47 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7193 (mp0) outliers start: 60 outliers final: 44 residues processed: 319 average time/residue: 0.2772 time to fit residues: 110.6538 Evaluate side-chains 335 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8096 Z= 0.209 Angle : 0.597 7.485 10997 Z= 0.312 Chirality : 0.044 0.210 1265 Planarity : 0.003 0.050 1405 Dihedral : 4.088 18.663 1112 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 6.04 % Allowed : 34.91 % Favored : 59.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1008 helix: 1.97 (0.26), residues: 412 sheet: 0.20 (0.36), residues: 214 loop : -0.91 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.012 0.001 HIS C 362 PHE 0.018 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.012 0.001 ARG G 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6605 (t0) REVERT: A 119 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7154 (tp) REVERT: A 157 SER cc_start: 0.8655 (m) cc_final: 0.8214 (p) REVERT: A 179 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7409 (tpp-160) REVERT: A 183 LEU cc_start: 0.8779 (tt) cc_final: 0.8216 (tp) REVERT: A 246 VAL cc_start: 0.8492 (t) cc_final: 0.8256 (p) REVERT: B 22 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.7550 (ttm-80) REVERT: B 33 ILE cc_start: 0.9064 (tt) cc_final: 0.8840 (mp) REVERT: B 52 ARG cc_start: 0.7237 (mtm180) cc_final: 0.6975 (mtm180) REVERT: B 57 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8098 (ptpp) REVERT: B 118 ASP cc_start: 0.7816 (p0) cc_final: 0.7440 (p0) REVERT: B 136 SER cc_start: 0.8495 (p) cc_final: 0.8096 (m) REVERT: B 142 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6425 (p90) REVERT: B 161 SER cc_start: 0.8455 (m) cc_final: 0.8048 (p) REVERT: B 175 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7633 (mm-40) REVERT: B 217 MET cc_start: 0.7866 (mtt) cc_final: 0.7642 (mtt) REVERT: B 219 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7694 (mmt90) REVERT: B 258 ASP cc_start: 0.7871 (t0) cc_final: 0.6984 (t0) REVERT: B 283 ARG cc_start: 0.8260 (tpt-90) cc_final: 0.7714 (tpt-90) REVERT: B 298 ASP cc_start: 0.7685 (t70) cc_final: 0.6800 (t0) REVERT: C 232 ARG cc_start: 0.8721 (ttp-110) cc_final: 0.8471 (ttp-110) REVERT: C 271 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8250 (mmtp) REVERT: C 273 PHE cc_start: 0.8323 (t80) cc_final: 0.7752 (t80) REVERT: C 299 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: C 392 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7002 (mm-30) REVERT: G 13 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7831 (mtm110) REVERT: G 14 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8638 (pttm) REVERT: G 47 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: N 22 CYS cc_start: 0.5996 (OUTLIER) cc_final: 0.5776 (t) outliers start: 51 outliers final: 42 residues processed: 313 average time/residue: 0.2784 time to fit residues: 109.1156 Evaluate side-chains 326 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 12 GLN Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 HIS Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 29 PHE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107912 restraints weight = 13094.584| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.76 r_work: 0.3239 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8096 Z= 0.215 Angle : 0.603 8.467 10997 Z= 0.316 Chirality : 0.044 0.213 1265 Planarity : 0.003 0.049 1405 Dihedral : 4.094 18.281 1112 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.92 % Allowed : 34.67 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1008 helix: 1.99 (0.26), residues: 410 sheet: 0.23 (0.36), residues: 214 loop : -0.95 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.012 0.001 HIS C 362 PHE 0.019 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.012 0.001 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2545.59 seconds wall clock time: 46 minutes 41.69 seconds (2801.69 seconds total)