Starting phenix.real_space_refine on Tue May 13 20:01:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xqf_38575/05_2025/8xqf_38575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xqf_38575/05_2025/8xqf_38575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xqf_38575/05_2025/8xqf_38575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xqf_38575/05_2025/8xqf_38575.map" model { file = "/net/cci-nas-00/data/ceres_data/8xqf_38575/05_2025/8xqf_38575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xqf_38575/05_2025/8xqf_38575.cif" } resolution = 3.13 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= 0.030 sd= 1.306 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2113 atoms to isotropic. 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 69 5.16 5 C 5873 2.51 5 N 1564 2.21 5 O 1727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9233 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1810 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2450 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 294} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 109 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 9} Time building chain proxies: 5.75, per 1000 atoms: 0.62 Number of scatterers: 9233 At special positions: 0 Unit cell: (91.52, 122.72, 130, 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 69 16.00 O 1727 8.00 N 1564 7.00 C 5873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.03 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 39.1% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.545A pdb=" N ASN A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.602A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.648A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.682A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.069A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 35 through 55 Processing helix chain 'C' and resid 60 through 76 Processing helix chain 'R' and resid 24 through 56 Proline residue: R 32 - end of helix removed outlier: 4.601A pdb=" N THR R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL R 49 " --> pdb=" O GLY R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.365A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 98 through 132 removed outlier: 3.599A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 166 removed outlier: 4.103A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 166 " --> pdb=" O MET R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 166' Processing helix chain 'R' and resid 193 through 209 removed outlier: 4.243A pdb=" N GLY R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 229 removed outlier: 4.007A pdb=" N PHE R 223 " --> pdb=" O THR R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 261 removed outlier: 3.798A pdb=" N VAL R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR R 256 " --> pdb=" O VAL R 252 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 276 removed outlier: 3.553A pdb=" N THR R 269 " --> pdb=" O HIS R 265 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 276 " --> pdb=" O MET R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 Processing helix chain 'R' and resid 290 through 309 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 323 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.864A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.946A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.842A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.147A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.662A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.738A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.414A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.541A 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: 7.201A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.594A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.896A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.896A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 159 through 160 Processing sheet with id=AB4, first strand: chain 'S' and resid 186 through 189 removed outlier: 6.958A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1236 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: 2.94 Time building geometry restraints manager: 2.97 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: 2967 1.34 - 1.46: 2343 1.46 - 1.58: 4023 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 9434 Sorted by residual: bond pdb=" N ASP S 74 " pdb=" CA ASP S 74 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.17e+00 bond pdb=" C TRP R 279 " pdb=" N PRO R 280 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.34e-02 5.57e+03 4.99e+00 bond pdb=" C ASP S 74 " pdb=" N PRO S 75 " ideal model delta sigma weight residual 1.332 1.353 -0.021 1.30e-02 5.92e+03 2.71e+00 bond pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 1.233 1.247 -0.014 1.16e-02 7.43e+03 1.55e+00 bond pdb=" CB PRO R 213 " pdb=" CG PRO R 213 " ideal model delta sigma weight residual 1.492 1.430 0.062 5.00e-02 4.00e+02 1.53e+00 ... (remaining 9429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 12664 2.84 - 5.67: 99 5.67 - 8.51: 14 8.51 - 11.35: 5 11.35 - 14.18: 1 Bond angle restraints: 12783 Sorted by residual: angle pdb=" CA CYS R 181 " pdb=" CB CYS R 181 " pdb=" SG CYS R 181 " ideal model delta sigma weight residual 114.40 128.58 -14.18 2.30e+00 1.89e-01 3.80e+01 angle pdb=" CB MET R 162 " pdb=" CG MET R 162 " pdb=" SD MET R 162 " ideal model delta sigma weight residual 112.70 122.59 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB MET R 288 " pdb=" CG MET R 288 " pdb=" SD MET R 288 " ideal model delta sigma weight residual 112.70 122.53 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" CA PRO S 75 " pdb=" C PRO S 75 " pdb=" O PRO S 75 " ideal model delta sigma weight residual 121.34 117.84 3.50 1.14e+00 7.69e-01 9.45e+00 angle pdb=" C GLN R 180 " pdb=" N CYS R 181 " pdb=" CA CYS R 181 " ideal model delta sigma weight residual 122.87 118.49 4.38 1.44e+00 4.82e-01 9.25e+00 ... (remaining 12778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 4749 16.73 - 33.46: 606 33.46 - 50.19: 179 50.19 - 66.92: 50 66.92 - 83.65: 6 Dihedral angle restraints: 5590 sinusoidal: 2172 harmonic: 3418 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 176.65 -83.65 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 154.44 -61.44 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CA PHE R 210 " pdb=" C PHE R 210 " pdb=" N VAL R 211 " pdb=" CA VAL R 211 " ideal model delta harmonic sigma weight residual 180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1184 0.054 - 0.108: 225 0.108 - 0.162: 27 0.162 - 0.216: 2 0.216 - 0.270: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CG LEU R 259 " pdb=" CB LEU R 259 " pdb=" CD1 LEU R 259 " pdb=" CD2 LEU R 259 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA CYS R 181 " pdb=" N CYS R 181 " pdb=" C CYS R 181 " pdb=" CB CYS R 181 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO R 280 " pdb=" N PRO R 280 " pdb=" C PRO R 280 " pdb=" CB PRO R 280 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1437 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP S 73 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C ASP S 73 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP S 73 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP S 74 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 108 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C LEU R 108 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU R 108 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE R 109 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO S 236 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.029 5.00e-02 4.00e+02 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 242 2.68 - 3.24: 9161 3.24 - 3.79: 15306 3.79 - 4.35: 20014 4.35 - 4.90: 32811 Nonbonded interactions: 77534 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.129 3.040 nonbonded pdb=" ND2 ASN B 237 " pdb=" OD1 ASN B 239 " model vdw 2.165 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.180 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.210 3.120 ... (remaining 77529 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.670 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 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 : 0.004 0.062 9437 Z= 0.167 Angle : 0.680 14.184 12789 Z= 0.350 Chirality : 0.043 0.270 1440 Planarity : 0.004 0.052 1617 Dihedral : 16.727 81.208 3377 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 30.32 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.26), residues: 1161 helix: 1.26 (0.27), residues: 403 sheet: -0.88 (0.33), residues: 263 loop : -1.57 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 85 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.002 PHE A 250 TYR 0.025 0.002 TYR R 88 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.17175 ( 433) hydrogen bonds : angle 6.83035 ( 1236) SS BOND : bond 0.00859 ( 3) SS BOND : angle 2.90314 ( 6) covalent geometry : bond 0.00367 ( 9434) covalent geometry : angle 0.67706 (12783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6719 (ttmm) cc_final: 0.6474 (ttmm) REVERT: C 44 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7447 (tpp-160) REVERT: R 50 LEU cc_start: 0.6044 (mp) cc_final: 0.5772 (mm) REVERT: R 154 TRP cc_start: 0.6868 (m100) cc_final: 0.4924 (m100) REVERT: S 83 MET cc_start: 0.6604 (mpp) cc_final: 0.6311 (mtm) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2624 time to fit residues: 88.3698 Evaluate side-chains 258 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 104 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 237 ASN B 239 ASN B 259 GLN C 55 ASN R 46 ASN S 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.179598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.157287 restraints weight = 14220.701| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.36 r_work: 0.3889 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9437 Z= 0.166 Angle : 0.641 13.094 12789 Z= 0.333 Chirality : 0.043 0.218 1440 Planarity : 0.004 0.052 1617 Dihedral : 4.922 37.156 1280 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 5.07 % Allowed : 25.45 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 1161 helix: 1.34 (0.26), residues: 404 sheet: -0.95 (0.31), residues: 274 loop : -1.51 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 213 PHE 0.017 0.002 PHE R 283 TYR 0.018 0.002 TYR R 88 ARG 0.004 0.000 ARG D 2 Details of bonding type rmsd hydrogen bonds : bond 0.04711 ( 433) hydrogen bonds : angle 5.32153 ( 1236) SS BOND : bond 0.00650 ( 3) SS BOND : angle 2.37247 ( 6) covalent geometry : bond 0.00371 ( 9434) covalent geometry : angle 0.63935 (12783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 261 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6585 (tm-30) cc_final: 0.6307 (tm-30) REVERT: A 243 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6870 (mmm) REVERT: A 337 ASP cc_start: 0.6891 (m-30) cc_final: 0.6599 (m-30) REVERT: B 36 ASN cc_start: 0.7750 (m-40) cc_final: 0.7494 (m-40) REVERT: B 123 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8357 (mm) REVERT: C 44 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7488 (tpp-160) REVERT: R 108 LEU cc_start: 0.5639 (mt) cc_final: 0.5321 (mp) REVERT: R 154 TRP cc_start: 0.7070 (m100) cc_final: 0.5072 (m100) REVERT: S 83 MET cc_start: 0.6581 (mpp) cc_final: 0.6272 (mtm) REVERT: S 93 MET cc_start: 0.7598 (tpp) cc_final: 0.7082 (tpp) REVERT: S 95 TYR cc_start: 0.8173 (m-10) cc_final: 0.7903 (m-10) REVERT: S 99 SER cc_start: 0.7788 (m) cc_final: 0.7522 (p) outliers start: 51 outliers final: 28 residues processed: 289 average time/residue: 0.2429 time to fit residues: 92.7345 Evaluate side-chains 282 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 98 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 90 ASN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.179862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.157600 restraints weight = 14422.630| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.38 r_work: 0.3887 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9437 Z= 0.149 Angle : 0.631 13.317 12789 Z= 0.321 Chirality : 0.042 0.176 1440 Planarity : 0.004 0.052 1617 Dihedral : 4.860 32.682 1280 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 4.47 % Allowed : 26.84 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1161 helix: 1.29 (0.26), residues: 404 sheet: -0.99 (0.31), residues: 273 loop : -1.59 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.017 0.002 PHE R 283 TYR 0.017 0.001 TYR R 88 ARG 0.004 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 433) hydrogen bonds : angle 5.08053 ( 1236) SS BOND : bond 0.00754 ( 3) SS BOND : angle 2.08856 ( 6) covalent geometry : bond 0.00339 ( 9434) covalent geometry : angle 0.62920 (12783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6267 (tm-30) REVERT: A 308 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6206 (mt-10) REVERT: A 337 ASP cc_start: 0.6906 (m-30) cc_final: 0.6594 (m-30) REVERT: B 36 ASN cc_start: 0.7746 (m-40) cc_final: 0.7507 (m-40) REVERT: B 123 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8329 (mm) REVERT: B 186 ASP cc_start: 0.7142 (m-30) cc_final: 0.6939 (m-30) REVERT: C 44 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7474 (tpp-160) REVERT: C 61 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7719 (t) REVERT: R 65 ASP cc_start: 0.5993 (m-30) cc_final: 0.5699 (m-30) REVERT: R 113 MET cc_start: 0.6790 (ttp) cc_final: 0.6517 (ttp) REVERT: R 124 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7562 (t) REVERT: R 165 MET cc_start: 0.4482 (tmm) cc_final: 0.3831 (ptp) REVERT: S 63 THR cc_start: 0.7973 (p) cc_final: 0.7628 (t) REVERT: S 83 MET cc_start: 0.6403 (mpp) cc_final: 0.6016 (mtm) REVERT: S 99 SER cc_start: 0.7768 (m) cc_final: 0.7505 (p) outliers start: 45 outliers final: 34 residues processed: 278 average time/residue: 0.2528 time to fit residues: 92.2823 Evaluate side-chains 288 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 156 GLN B 239 ASN B 259 GLN B 340 ASN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.156948 restraints weight = 14256.561| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.36 r_work: 0.3883 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9437 Z= 0.161 Angle : 0.630 13.218 12789 Z= 0.320 Chirality : 0.043 0.185 1440 Planarity : 0.004 0.053 1617 Dihedral : 4.902 33.919 1280 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 5.96 % Allowed : 26.14 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1161 helix: 1.23 (0.26), residues: 407 sheet: -0.99 (0.31), residues: 274 loop : -1.54 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 PHE 0.016 0.002 PHE R 257 TYR 0.019 0.002 TYR R 88 ARG 0.004 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 433) hydrogen bonds : angle 5.09039 ( 1236) SS BOND : bond 0.00651 ( 3) SS BOND : angle 1.18791 ( 6) covalent geometry : bond 0.00367 ( 9434) covalent geometry : angle 0.62954 (12783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8034 (t) cc_final: 0.7825 (t) REVERT: A 25 GLU cc_start: 0.6639 (tm-30) cc_final: 0.6231 (tm-30) REVERT: A 308 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6293 (mt-10) REVERT: B 36 ASN cc_start: 0.7735 (m-40) cc_final: 0.7506 (m-40) REVERT: B 68 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7455 (ttt180) REVERT: B 123 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 186 ASP cc_start: 0.7117 (m-30) cc_final: 0.6894 (m-30) REVERT: C 44 ARG cc_start: 0.8007 (tpp-160) cc_final: 0.7470 (tpp-160) REVERT: R 35 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.5871 (m-80) REVERT: R 65 ASP cc_start: 0.6087 (m-30) cc_final: 0.5775 (m-30) REVERT: R 113 MET cc_start: 0.6765 (ttp) cc_final: 0.6493 (ttp) REVERT: R 120 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7610 (mp) REVERT: R 124 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7567 (t) REVERT: R 165 MET cc_start: 0.4612 (tmm) cc_final: 0.3957 (ptp) REVERT: R 253 LEU cc_start: 0.7735 (mt) cc_final: 0.7468 (mm) REVERT: S 63 THR cc_start: 0.7992 (p) cc_final: 0.7654 (t) REVERT: S 83 MET cc_start: 0.6506 (mpp) cc_final: 0.6170 (mtm) REVERT: S 95 TYR cc_start: 0.8182 (m-10) cc_final: 0.7968 (m-10) REVERT: S 99 SER cc_start: 0.7815 (m) cc_final: 0.7573 (p) outliers start: 60 outliers final: 43 residues processed: 282 average time/residue: 0.2450 time to fit residues: 91.2450 Evaluate side-chains 296 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.180539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.158431 restraints weight = 14299.112| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.37 r_work: 0.3903 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9437 Z= 0.129 Angle : 0.621 13.221 12789 Z= 0.310 Chirality : 0.042 0.172 1440 Planarity : 0.004 0.053 1617 Dihedral : 4.778 32.930 1280 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 5.47 % Allowed : 25.75 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.26), residues: 1161 helix: 1.34 (0.26), residues: 407 sheet: -0.94 (0.31), residues: 275 loop : -1.50 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.018 0.002 PHE A 250 TYR 0.021 0.001 TYR R 88 ARG 0.004 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 433) hydrogen bonds : angle 4.93744 ( 1236) SS BOND : bond 0.00816 ( 3) SS BOND : angle 2.44490 ( 6) covalent geometry : bond 0.00296 ( 9434) covalent geometry : angle 0.61888 (12783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 251 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6292 (tm-30) REVERT: A 275 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: A 308 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6218 (mt-10) REVERT: B 36 ASN cc_start: 0.7700 (m-40) cc_final: 0.7446 (m-40) REVERT: B 68 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7370 (ttt180) REVERT: B 186 ASP cc_start: 0.7119 (m-30) cc_final: 0.6884 (m-30) REVERT: C 61 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7727 (t) REVERT: R 35 TYR cc_start: 0.6641 (m-10) cc_final: 0.5908 (m-80) REVERT: R 65 ASP cc_start: 0.6101 (m-30) cc_final: 0.5857 (m-30) REVERT: R 113 MET cc_start: 0.6801 (ttp) cc_final: 0.6550 (ttp) REVERT: R 120 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7583 (mp) REVERT: R 124 SER cc_start: 0.7787 (OUTLIER) cc_final: 0.7553 (t) REVERT: R 165 MET cc_start: 0.4187 (tmm) cc_final: 0.3749 (mmm) REVERT: S 63 THR cc_start: 0.8002 (p) cc_final: 0.7669 (t) REVERT: S 99 SER cc_start: 0.7747 (m) cc_final: 0.7506 (p) REVERT: D 2 ARG cc_start: 0.6372 (ttp80) cc_final: 0.5981 (ttp80) outliers start: 55 outliers final: 39 residues processed: 277 average time/residue: 0.2426 time to fit residues: 88.3299 Evaluate side-chains 289 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 259 LEU Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 0.0040 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 259 GLN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.158105 restraints weight = 14284.091| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.35 r_work: 0.3896 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9437 Z= 0.139 Angle : 0.628 16.473 12789 Z= 0.312 Chirality : 0.042 0.164 1440 Planarity : 0.004 0.054 1617 Dihedral : 4.783 34.309 1280 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.51 % Favored : 94.40 % Rotamer: Outliers : 5.67 % Allowed : 26.44 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1161 helix: 1.36 (0.26), residues: 407 sheet: -0.90 (0.31), residues: 275 loop : -1.47 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.021 0.002 PHE A 250 TYR 0.020 0.001 TYR R 88 ARG 0.005 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 433) hydrogen bonds : angle 4.93220 ( 1236) SS BOND : bond 0.00701 ( 3) SS BOND : angle 2.08796 ( 6) covalent geometry : bond 0.00319 ( 9434) covalent geometry : angle 0.62614 (12783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 248 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8070 (t) cc_final: 0.7858 (t) REVERT: A 17 LYS cc_start: 0.7611 (mmtt) cc_final: 0.7393 (mmtt) REVERT: A 25 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6281 (tm-30) REVERT: A 270 LYS cc_start: 0.7521 (mttp) cc_final: 0.7252 (mttp) REVERT: A 273 LEU cc_start: 0.7793 (mt) cc_final: 0.7575 (mt) REVERT: A 275 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: A 308 GLU cc_start: 0.6449 (mt-10) cc_final: 0.6200 (mt-10) REVERT: B 36 ASN cc_start: 0.7710 (m-40) cc_final: 0.7455 (m-40) REVERT: B 68 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7488 (ttt180) REVERT: B 129 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7115 (mmt180) REVERT: B 186 ASP cc_start: 0.7131 (m-30) cc_final: 0.6846 (m-30) REVERT: R 35 TYR cc_start: 0.6769 (OUTLIER) cc_final: 0.5862 (m-80) REVERT: R 65 ASP cc_start: 0.6175 (m-30) cc_final: 0.5933 (m-30) REVERT: R 113 MET cc_start: 0.6833 (ttp) cc_final: 0.6556 (ttp) REVERT: R 120 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7570 (mp) REVERT: R 124 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7555 (t) REVERT: R 253 LEU cc_start: 0.7730 (mt) cc_final: 0.7503 (mm) REVERT: S 63 THR cc_start: 0.8008 (p) cc_final: 0.7690 (t) outliers start: 57 outliers final: 42 residues processed: 273 average time/residue: 0.2465 time to fit residues: 88.7782 Evaluate side-chains 294 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 246 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.178912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.156442 restraints weight = 14410.918| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.38 r_work: 0.3873 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9437 Z= 0.170 Angle : 0.667 18.024 12789 Z= 0.329 Chirality : 0.044 0.347 1440 Planarity : 0.004 0.054 1617 Dihedral : 4.882 35.022 1280 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 5.96 % Allowed : 26.94 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1161 helix: 1.25 (0.26), residues: 408 sheet: -0.86 (0.31), residues: 273 loop : -1.44 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 85 HIS 0.002 0.001 HIS B 183 PHE 0.025 0.002 PHE A 250 TYR 0.024 0.002 TYR R 88 ARG 0.005 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 433) hydrogen bonds : angle 4.95809 ( 1236) SS BOND : bond 0.00721 ( 3) SS BOND : angle 1.82655 ( 6) covalent geometry : bond 0.00389 ( 9434) covalent geometry : angle 0.66607 (12783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7385 (mmtt) REVERT: A 25 GLU cc_start: 0.6618 (tm-30) cc_final: 0.6214 (tm-30) REVERT: A 270 LYS cc_start: 0.7538 (mttp) cc_final: 0.7260 (mttp) REVERT: A 273 LEU cc_start: 0.7837 (mt) cc_final: 0.7615 (mt) REVERT: A 275 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: A 308 GLU cc_start: 0.6391 (mt-10) cc_final: 0.6136 (mt-10) REVERT: B 36 ASN cc_start: 0.7683 (m-40) cc_final: 0.7430 (m-40) REVERT: B 68 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7436 (ttt180) REVERT: B 129 ARG cc_start: 0.7507 (mtt-85) cc_final: 0.7091 (mmt180) REVERT: B 186 ASP cc_start: 0.7079 (m-30) cc_final: 0.6763 (m-30) REVERT: C 61 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7735 (t) REVERT: R 35 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5837 (m-80) REVERT: R 113 MET cc_start: 0.6836 (ttp) cc_final: 0.6557 (ttp) REVERT: R 120 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7570 (mp) REVERT: R 124 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7574 (t) REVERT: R 165 MET cc_start: 0.3668 (tpp) cc_final: 0.2503 (mpp) REVERT: R 253 LEU cc_start: 0.7805 (mt) cc_final: 0.7565 (mm) REVERT: S 63 THR cc_start: 0.8059 (p) cc_final: 0.7739 (t) REVERT: S 67 ARG cc_start: 0.6613 (mtm110) cc_final: 0.6292 (mtm110) REVERT: S 99 SER cc_start: 0.7798 (m) cc_final: 0.7569 (p) outliers start: 60 outliers final: 46 residues processed: 283 average time/residue: 0.2511 time to fit residues: 94.8215 Evaluate side-chains 304 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 252 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 59 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 104 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 220 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.156614 restraints weight = 14452.821| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.38 r_work: 0.3871 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9437 Z= 0.165 Angle : 0.674 18.318 12789 Z= 0.329 Chirality : 0.044 0.265 1440 Planarity : 0.004 0.054 1617 Dihedral : 4.886 35.775 1280 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 6.06 % Allowed : 27.04 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1161 helix: 1.21 (0.26), residues: 408 sheet: -0.87 (0.31), residues: 273 loop : -1.45 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 183 PHE 0.022 0.002 PHE A 250 TYR 0.024 0.002 TYR R 88 ARG 0.005 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 433) hydrogen bonds : angle 4.99166 ( 1236) SS BOND : bond 0.00659 ( 3) SS BOND : angle 1.72788 ( 6) covalent geometry : bond 0.00379 ( 9434) covalent geometry : angle 0.67317 (12783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 253 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7333 (mmtt) REVERT: A 25 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6219 (tm-30) REVERT: A 270 LYS cc_start: 0.7535 (mttp) cc_final: 0.7262 (mttp) REVERT: A 273 LEU cc_start: 0.7844 (mt) cc_final: 0.7627 (mt) REVERT: A 275 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: A 308 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6147 (mt-10) REVERT: B 36 ASN cc_start: 0.7678 (m-40) cc_final: 0.7441 (m-40) REVERT: B 68 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7439 (ttt180) REVERT: B 186 ASP cc_start: 0.7090 (m-30) cc_final: 0.6699 (m-30) REVERT: R 35 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: R 120 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7569 (mp) REVERT: R 124 SER cc_start: 0.7797 (OUTLIER) cc_final: 0.7567 (t) REVERT: R 165 MET cc_start: 0.3610 (tpp) cc_final: 0.2500 (mpp) REVERT: R 253 LEU cc_start: 0.7789 (mt) cc_final: 0.7504 (mm) REVERT: S 63 THR cc_start: 0.8065 (p) cc_final: 0.7757 (t) REVERT: S 67 ARG cc_start: 0.6616 (mtm110) cc_final: 0.6277 (mtm110) REVERT: S 99 SER cc_start: 0.7820 (m) cc_final: 0.7562 (p) outliers start: 61 outliers final: 44 residues processed: 285 average time/residue: 0.2357 time to fit residues: 89.2401 Evaluate side-chains 300 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 chunk 35 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 220 GLN B 259 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157845 restraints weight = 14270.533| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.38 r_work: 0.3890 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9437 Z= 0.134 Angle : 0.654 18.568 12789 Z= 0.319 Chirality : 0.042 0.215 1440 Planarity : 0.004 0.053 1617 Dihedral : 4.816 36.558 1280 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 5.67 % Allowed : 27.14 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.26), residues: 1161 helix: 1.27 (0.26), residues: 410 sheet: -0.82 (0.31), residues: 279 loop : -1.39 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 PHE 0.019 0.002 PHE A 250 TYR 0.025 0.001 TYR R 88 ARG 0.005 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 433) hydrogen bonds : angle 4.87692 ( 1236) SS BOND : bond 0.00577 ( 3) SS BOND : angle 1.53758 ( 6) covalent geometry : bond 0.00310 ( 9434) covalent geometry : angle 0.65294 (12783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7322 (mmtt) REVERT: A 25 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6268 (tm-30) REVERT: A 275 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: A 308 GLU cc_start: 0.6402 (mt-10) cc_final: 0.6154 (mt-10) REVERT: B 36 ASN cc_start: 0.7681 (m-40) cc_final: 0.7447 (m-40) REVERT: B 68 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7395 (ttt180) REVERT: B 129 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7080 (mmt180) REVERT: B 186 ASP cc_start: 0.7073 (m-30) cc_final: 0.6713 (m-30) REVERT: R 35 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.5928 (m-80) REVERT: R 120 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7571 (mp) REVERT: R 124 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7562 (t) REVERT: R 165 MET cc_start: 0.3586 (tpp) cc_final: 0.2636 (mtm) REVERT: S 63 THR cc_start: 0.8083 (p) cc_final: 0.7773 (t) REVERT: S 67 ARG cc_start: 0.6599 (mtm110) cc_final: 0.6278 (mtm110) REVERT: S 83 MET cc_start: 0.6611 (mpp) cc_final: 0.6147 (mtm) outliers start: 57 outliers final: 47 residues processed: 276 average time/residue: 0.2411 time to fit residues: 87.4650 Evaluate side-chains 294 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 0.0170 chunk 67 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 220 GLN B 259 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.178286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155711 restraints weight = 14442.032| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.39 r_work: 0.3861 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9437 Z= 0.194 Angle : 0.714 19.580 12789 Z= 0.347 Chirality : 0.045 0.219 1440 Planarity : 0.004 0.055 1617 Dihedral : 4.973 36.653 1280 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 5.17 % Allowed : 27.93 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.25), residues: 1161 helix: 1.12 (0.26), residues: 409 sheet: -0.83 (0.31), residues: 269 loop : -1.45 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 85 HIS 0.003 0.001 HIS B 311 PHE 0.024 0.002 PHE A 250 TYR 0.022 0.002 TYR R 35 ARG 0.006 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 433) hydrogen bonds : angle 5.04995 ( 1236) SS BOND : bond 0.00794 ( 3) SS BOND : angle 1.61808 ( 6) covalent geometry : bond 0.00447 ( 9434) covalent geometry : angle 0.71324 (12783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7339 (mmtt) REVERT: A 25 GLU cc_start: 0.6647 (tm-30) cc_final: 0.6250 (tm-30) REVERT: A 275 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7241 (pt0) REVERT: A 308 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6152 (mt-10) REVERT: B 36 ASN cc_start: 0.7670 (m-40) cc_final: 0.7349 (m-40) REVERT: B 68 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7545 (ttt180) REVERT: B 129 ARG cc_start: 0.7412 (mtt-85) cc_final: 0.7076 (mmt180) REVERT: B 186 ASP cc_start: 0.7064 (m-30) cc_final: 0.6679 (m-30) REVERT: B 197 ARG cc_start: 0.6709 (ptt180) cc_final: 0.6211 (ptt-90) REVERT: C 44 ARG cc_start: 0.7915 (tpp-160) cc_final: 0.7406 (tpp-160) REVERT: R 35 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.5836 (m-80) REVERT: R 120 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7571 (mp) REVERT: R 124 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7580 (t) REVERT: S 63 THR cc_start: 0.8107 (p) cc_final: 0.7820 (t) REVERT: S 67 ARG cc_start: 0.6650 (mtm110) cc_final: 0.6336 (mtm110) REVERT: S 99 SER cc_start: 0.7825 (m) cc_final: 0.7572 (p) outliers start: 52 outliers final: 44 residues processed: 282 average time/residue: 0.2413 time to fit residues: 89.9837 Evaluate side-chains 300 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain R residue 35 TYR Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 55 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 272 MET Chi-restraints excluded: chain R residue 273 LEU Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 298 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain D residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 183 HIS B 220 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.179136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.156827 restraints weight = 14392.345| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.38 r_work: 0.3874 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9437 Z= 0.158 Angle : 0.697 18.831 12789 Z= 0.336 Chirality : 0.043 0.233 1440 Planarity : 0.004 0.053 1617 Dihedral : 4.930 36.906 1280 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 5.47 % Allowed : 28.23 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1161 helix: 1.19 (0.26), residues: 406 sheet: -0.81 (0.31), residues: 279 loop : -1.44 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS S 35 PHE 0.023 0.002 PHE A 250 TYR 0.026 0.001 TYR R 88 ARG 0.005 0.000 ARG B 283 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 433) hydrogen bonds : angle 4.94889 ( 1236) SS BOND : bond 0.00641 ( 3) SS BOND : angle 1.50586 ( 6) covalent geometry : bond 0.00365 ( 9434) covalent geometry : angle 0.69685 (12783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5117.70 seconds wall clock time: 89 minutes 20.75 seconds (5360.75 seconds total)