Starting phenix.real_space_refine on Mon Apr 28 19:05:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfw_61442/04_2025/9jfw_61442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfw_61442/04_2025/9jfw_61442.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/9jfw_61442/04_2025/9jfw_61442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfw_61442/04_2025/9jfw_61442.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfw_61442/04_2025/9jfw_61442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfw_61442/04_2025/9jfw_61442.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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5080 2.51 5 N 1379 2.21 5 O 1480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7990 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1776 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2522 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 421 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 951 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2320 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 280} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 5.06, per 1000 atoms: 0.63 Number of scatterers: 7990 At special positions: 0 Unit cell: (72.8, 99.84, 135.2, 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 51 16.00 O 1480 8.00 N 1379 7.00 C 5080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 41.2% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.782A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.816A pdb=" N ASP A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.869A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.546A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 29 through 44 removed outlier: 4.193A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 14 through 48 Proline residue: R 20 - end of helix removed outlier: 4.028A pdb=" N LEU R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 79 removed outlier: 4.158A pdb=" N VAL R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 98 Processing helix chain 'R' and resid 99 through 120 Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 150 Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.883A pdb=" N PHE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 150 through 155' Processing helix chain 'R' and resid 175 through 189 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 removed outlier: 4.234A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 276 removed outlier: 5.558A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 273 " --> pdb=" O HIS R 269 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.508A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.467A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.545A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.070A 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: 6.572A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.967A 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: 6.721A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.195A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.529A 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: 6.667A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.411A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 59 through 60 removed outlier: 5.238A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 68 through 69 Processing sheet with id=AB2, first strand: chain 'N' and resid 72 through 73 Processing sheet with id=AB3, first strand: chain 'R' and resid 160 through 161 removed outlier: 4.087A pdb=" N HIS R 165 " --> pdb=" O ASP R 161 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1107 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: 2.11 Time building geometry restraints manager: 2.48 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: 2615 1.34 - 1.46: 1779 1.46 - 1.58: 3706 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 8168 Sorted by residual: bond pdb=" CA SER R 266 " pdb=" CB SER R 266 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.23e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" CA SER R 270 " pdb=" CB SER R 270 " ideal model delta sigma weight residual 1.534 1.477 0.057 1.71e-02 3.42e+03 1.11e+01 bond pdb=" CA SER R 271 " pdb=" CB SER R 271 " ideal model delta sigma weight residual 1.534 1.480 0.054 1.71e-02 3.42e+03 1.00e+01 bond pdb=" N PRO B 236 " pdb=" CD PRO B 236 " ideal model delta sigma weight residual 1.473 1.506 -0.033 1.40e-02 5.10e+03 5.64e+00 ... (remaining 8163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 10842 1.77 - 3.55: 215 3.55 - 5.32: 36 5.32 - 7.10: 12 7.10 - 8.87: 2 Bond angle restraints: 11107 Sorted by residual: angle pdb=" N LEU R 272 " pdb=" CA LEU R 272 " pdb=" C LEU R 272 " ideal model delta sigma weight residual 112.23 103.36 8.87 1.26e+00 6.30e-01 4.96e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 112.96 107.60 5.36 1.00e+00 1.00e+00 2.88e+01 angle pdb=" N SER R 270 " pdb=" CA SER R 270 " pdb=" C SER R 270 " ideal model delta sigma weight residual 113.38 107.22 6.16 1.23e+00 6.61e-01 2.51e+01 angle pdb=" N PHE R 167 " pdb=" CA PHE R 167 " pdb=" C PHE R 167 " ideal model delta sigma weight residual 110.19 116.29 -6.10 1.24e+00 6.50e-01 2.42e+01 angle pdb=" CA PHE R 172 " pdb=" CB PHE R 172 " pdb=" CG PHE R 172 " ideal model delta sigma weight residual 113.80 109.14 4.66 1.00e+00 1.00e+00 2.17e+01 ... (remaining 11102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4186 17.84 - 35.67: 451 35.67 - 53.51: 119 53.51 - 71.34: 38 71.34 - 89.18: 6 Dihedral angle restraints: 4800 sinusoidal: 1783 harmonic: 3017 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 130.16 -37.16 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" C PHE R 172 " pdb=" N PHE R 172 " pdb=" CA PHE R 172 " pdb=" CB PHE R 172 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1006 0.049 - 0.099: 197 0.099 - 0.148: 46 0.148 - 0.197: 4 0.197 - 0.246: 3 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA PHE R 172 " pdb=" N PHE R 172 " pdb=" C PHE R 172 " pdb=" CB PHE R 172 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE B 270 " pdb=" N ILE B 270 " pdb=" C ILE B 270 " pdb=" CB ILE B 270 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LYS A 271 " pdb=" N LYS A 271 " pdb=" C LYS A 271 " pdb=" CB LYS A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1253 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 99 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C THR R 99 " -0.048 2.00e-02 2.50e+03 pdb=" O THR R 99 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN R 100 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 268 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.33e+00 pdb=" C TYR R 268 " -0.032 2.00e-02 2.50e+03 pdb=" O TYR R 268 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS R 269 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO C 49 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.022 5.00e-02 4.00e+02 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 252 2.70 - 3.25: 8042 3.25 - 3.80: 13529 3.80 - 4.35: 16917 4.35 - 4.90: 28216 Nonbonded interactions: 66956 Sorted by model distance: nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.193 3.040 nonbonded pdb=" OG SER N 112 " pdb=" O THR N 114 " model vdw 2.195 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR A 391 " pdb=" OE1 GLU R 51 " model vdw 2.218 3.040 ... (remaining 66951 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.690 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.003 0.057 8170 Z= 0.181 Angle : 0.619 8.870 11111 Z= 0.368 Chirality : 0.043 0.246 1256 Planarity : 0.004 0.039 1425 Dihedral : 16.744 89.175 2844 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.48 % Allowed : 25.99 % Favored : 73.53 % Cbeta Deviations : 0.10 % 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: -0.38 (0.26), residues: 1021 helix: 1.55 (0.27), residues: 388 sheet: -0.76 (0.35), residues: 209 loop : -1.72 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS R 165 PHE 0.018 0.002 PHE R 172 TYR 0.012 0.001 TYR R 268 ARG 0.005 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.14647 ( 384) hydrogen bonds : angle 6.11022 ( 1107) SS BOND : bond 0.00175 ( 2) SS BOND : angle 1.02051 ( 4) covalent geometry : bond 0.00315 ( 8168) covalent geometry : angle 0.61931 (11107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6710 (tm-30) cc_final: 0.6373 (tm-30) REVERT: A 240 ASP cc_start: 0.6922 (p0) cc_final: 0.6646 (p0) REVERT: A 380 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7280 (ttp80) REVERT: A 385 ARG cc_start: 0.7448 (mtp85) cc_final: 0.7226 (mmm160) REVERT: B 48 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.7038 (mmt-90) REVERT: B 59 TYR cc_start: 0.7835 (m-80) cc_final: 0.7370 (m-80) REVERT: B 78 LYS cc_start: 0.8117 (tppp) cc_final: 0.7795 (tppp) REVERT: B 176 GLN cc_start: 0.8659 (mt0) cc_final: 0.8344 (mt0) REVERT: B 205 ASP cc_start: 0.7383 (p0) cc_final: 0.7147 (p0) REVERT: B 212 ASP cc_start: 0.7113 (t0) cc_final: 0.6867 (t0) REVERT: B 226 GLU cc_start: 0.7753 (pt0) cc_final: 0.7271 (pt0) REVERT: B 303 ASP cc_start: 0.7417 (m-30) cc_final: 0.7172 (m-30) REVERT: N 19 ARG cc_start: 0.6723 (ppt-90) cc_final: 0.6372 (ppt-90) REVERT: N 60 TYR cc_start: 0.7356 (m-80) cc_final: 0.6870 (m-80) REVERT: R 23 LEU cc_start: 0.6864 (mp) cc_final: 0.6485 (mp) REVERT: R 40 TRP cc_start: 0.7015 (t-100) cc_final: 0.6728 (t-100) outliers start: 4 outliers final: 2 residues processed: 180 average time/residue: 0.2903 time to fit residues: 64.8495 Evaluate side-chains 172 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS A 294 GLN A 371 ASN B 88 ASN B 237 ASN R 165 HIS R 269 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.142015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127570 restraints weight = 11374.406| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.74 r_work: 0.3569 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8170 Z= 0.163 Angle : 0.564 6.767 11111 Z= 0.304 Chirality : 0.043 0.171 1256 Planarity : 0.004 0.042 1425 Dihedral : 5.053 58.648 1127 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.81 % Allowed : 22.62 % Favored : 72.56 % 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: -0.17 (0.26), residues: 1021 helix: 1.76 (0.27), residues: 386 sheet: -0.88 (0.35), residues: 217 loop : -1.49 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS R 241 PHE 0.020 0.002 PHE R 97 TYR 0.016 0.002 TYR R 76 ARG 0.005 0.001 ARG R 209 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 384) hydrogen bonds : angle 4.59236 ( 1107) SS BOND : bond 0.00132 ( 2) SS BOND : angle 1.28207 ( 4) covalent geometry : bond 0.00368 ( 8168) covalent geometry : angle 0.56348 (11107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6728 (tm-30) REVERT: A 36 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 175 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7740 (mm-40) REVERT: B 176 GLN cc_start: 0.8615 (mt0) cc_final: 0.8254 (mt0) REVERT: B 243 THR cc_start: 0.7930 (p) cc_final: 0.7725 (p) REVERT: B 261 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7289 (mp) REVERT: N 60 TYR cc_start: 0.7359 (m-80) cc_final: 0.6909 (m-80) REVERT: R 65 LEU cc_start: 0.8183 (mp) cc_final: 0.7962 (mp) REVERT: R 181 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7174 (tmm) REVERT: R 251 TYR cc_start: 0.7998 (t80) cc_final: 0.7477 (t80) outliers start: 40 outliers final: 19 residues processed: 202 average time/residue: 0.2767 time to fit residues: 69.9263 Evaluate side-chains 196 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 239 ASN ** 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 = 0.3820 r_free = 0.3820 target = 0.139128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124750 restraints weight = 11420.834| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.73 r_work: 0.3532 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8170 Z= 0.209 Angle : 0.583 7.146 11111 Z= 0.314 Chirality : 0.044 0.173 1256 Planarity : 0.005 0.058 1425 Dihedral : 4.722 41.787 1125 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.09 % Allowed : 22.74 % Favored : 73.16 % 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: -0.18 (0.26), residues: 1021 helix: 1.64 (0.27), residues: 388 sheet: -0.65 (0.36), residues: 201 loop : -1.52 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.002 PHE R 97 TYR 0.024 0.002 TYR R 268 ARG 0.006 0.001 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 384) hydrogen bonds : angle 4.53440 ( 1107) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.47940 ( 4) covalent geometry : bond 0.00475 ( 8168) covalent geometry : angle 0.58221 (11107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6750 (tm-30) REVERT: A 27 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 49 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7833 (ttm170) REVERT: B 176 GLN cc_start: 0.8641 (mt0) cc_final: 0.8325 (mt0) REVERT: B 205 ASP cc_start: 0.7168 (p0) cc_final: 0.6931 (p0) REVERT: B 234 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: B 243 THR cc_start: 0.7891 (p) cc_final: 0.7690 (p) REVERT: B 274 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7924 (m) REVERT: N 60 TYR cc_start: 0.7464 (m-80) cc_final: 0.7066 (m-80) REVERT: N 72 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7086 (mtp180) REVERT: R 65 LEU cc_start: 0.8292 (mp) cc_final: 0.8079 (mp) REVERT: R 170 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6834 (pp20) REVERT: R 181 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7198 (tmm) REVERT: R 251 TYR cc_start: 0.8057 (t80) cc_final: 0.7557 (t80) outliers start: 34 outliers final: 18 residues processed: 209 average time/residue: 0.2564 time to fit residues: 67.6442 Evaluate side-chains 203 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.0040 chunk 66 optimal weight: 0.0970 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127240 restraints weight = 11412.661| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.73 r_work: 0.3569 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8170 Z= 0.128 Angle : 0.529 7.099 11111 Z= 0.283 Chirality : 0.041 0.153 1256 Planarity : 0.004 0.058 1425 Dihedral : 4.466 39.712 1125 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.97 % Allowed : 23.47 % Favored : 72.56 % 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: 0.01 (0.26), residues: 1021 helix: 1.89 (0.27), residues: 383 sheet: -0.54 (0.36), residues: 199 loop : -1.47 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE R 19 TYR 0.021 0.001 TYR R 268 ARG 0.004 0.000 ARG N 19 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 384) hydrogen bonds : angle 4.32610 ( 1107) SS BOND : bond 0.00181 ( 2) SS BOND : angle 1.05697 ( 4) covalent geometry : bond 0.00283 ( 8168) covalent geometry : angle 0.52881 (11107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 27 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 36 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8453 (p) REVERT: A 271 LYS cc_start: 0.7579 (mmtt) cc_final: 0.7046 (mmtp) REVERT: B 61 MET cc_start: 0.7854 (ppp) cc_final: 0.7288 (ppp) REVERT: B 175 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7631 (mm-40) REVERT: B 176 GLN cc_start: 0.8609 (mt0) cc_final: 0.8303 (mt0) REVERT: B 205 ASP cc_start: 0.7073 (p0) cc_final: 0.6848 (p0) REVERT: B 226 GLU cc_start: 0.7568 (pt0) cc_final: 0.7147 (pt0) REVERT: B 234 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: B 243 THR cc_start: 0.7873 (p) cc_final: 0.7663 (p) REVERT: B 274 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7847 (m) REVERT: N 60 TYR cc_start: 0.7341 (m-80) cc_final: 0.7003 (m-80) REVERT: R 65 LEU cc_start: 0.8333 (mp) cc_final: 0.8120 (mp) REVERT: R 170 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6703 (pp20) REVERT: R 181 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7203 (tmm) outliers start: 33 outliers final: 17 residues processed: 207 average time/residue: 0.2672 time to fit residues: 70.0739 Evaluate side-chains 198 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** R 269 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 = 0.3837 r_free = 0.3837 target = 0.140717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126066 restraints weight = 11372.215| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.85 r_work: 0.3541 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8170 Z= 0.142 Angle : 0.536 6.918 11111 Z= 0.288 Chirality : 0.042 0.183 1256 Planarity : 0.005 0.070 1425 Dihedral : 4.432 37.004 1125 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.93 % Allowed : 22.26 % Favored : 72.80 % 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: 0.07 (0.27), residues: 1021 helix: 1.94 (0.27), residues: 383 sheet: -0.51 (0.37), residues: 199 loop : -1.43 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.008 0.001 HIS R 269 PHE 0.024 0.002 PHE A 363 TYR 0.019 0.001 TYR R 268 ARG 0.010 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 384) hydrogen bonds : angle 4.31938 ( 1107) SS BOND : bond 0.00240 ( 2) SS BOND : angle 1.12486 ( 4) covalent geometry : bond 0.00317 ( 8168) covalent geometry : angle 0.53606 (11107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6728 (tm-30) REVERT: A 36 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8378 (p) REVERT: A 271 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7356 (mmtp) REVERT: B 61 MET cc_start: 0.7856 (ppp) cc_final: 0.7331 (ppp) REVERT: B 175 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7667 (mm-40) REVERT: B 176 GLN cc_start: 0.8649 (mt0) cc_final: 0.8320 (mt0) REVERT: B 205 ASP cc_start: 0.7042 (p0) cc_final: 0.6772 (p0) REVERT: B 226 GLU cc_start: 0.7553 (pt0) cc_final: 0.7207 (pt0) REVERT: B 234 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7768 (m-80) REVERT: B 274 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7919 (m) REVERT: B 293 ASN cc_start: 0.7862 (t0) cc_final: 0.7500 (m-40) REVERT: N 60 TYR cc_start: 0.7429 (m-80) cc_final: 0.7036 (m-80) REVERT: R 170 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6875 (pp20) REVERT: R 181 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7159 (tmm) REVERT: R 237 PHE cc_start: 0.7421 (m-10) cc_final: 0.6989 (m-10) outliers start: 41 outliers final: 23 residues processed: 204 average time/residue: 0.2824 time to fit residues: 72.3855 Evaluate side-chains 207 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 0.0010 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 75 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN R 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.142658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127963 restraints weight = 11187.581| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.83 r_work: 0.3551 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8170 Z= 0.146 Angle : 0.545 8.248 11111 Z= 0.291 Chirality : 0.042 0.185 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.428 35.999 1125 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.69 % Allowed : 24.07 % Favored : 71.24 % 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: 0.01 (0.27), residues: 1021 helix: 1.95 (0.27), residues: 382 sheet: -0.77 (0.36), residues: 215 loop : -1.40 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.008 0.001 HIS R 269 PHE 0.020 0.002 PHE A 363 TYR 0.017 0.001 TYR R 268 ARG 0.008 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 384) hydrogen bonds : angle 4.31898 ( 1107) SS BOND : bond 0.00255 ( 2) SS BOND : angle 1.25865 ( 4) covalent geometry : bond 0.00328 ( 8168) covalent geometry : angle 0.54448 (11107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 36 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8406 (p) REVERT: B 61 MET cc_start: 0.7834 (ppp) cc_final: 0.7420 (ppp) REVERT: B 68 ARG cc_start: 0.8037 (ttt-90) cc_final: 0.7766 (ttt-90) REVERT: B 175 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7708 (mm-40) REVERT: B 176 GLN cc_start: 0.8708 (mt0) cc_final: 0.8390 (mt0) REVERT: B 226 GLU cc_start: 0.7568 (pt0) cc_final: 0.7358 (pt0) REVERT: B 234 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: B 274 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7871 (m) REVERT: B 293 ASN cc_start: 0.7834 (t0) cc_final: 0.7466 (m-40) REVERT: N 60 TYR cc_start: 0.7490 (m-80) cc_final: 0.7077 (m-80) REVERT: R 83 TRP cc_start: 0.8376 (t-100) cc_final: 0.8108 (t-100) REVERT: R 170 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6819 (pp20) REVERT: R 181 MET cc_start: 0.7843 (mmm) cc_final: 0.7161 (tmm) outliers start: 39 outliers final: 30 residues processed: 212 average time/residue: 0.2565 time to fit residues: 68.9828 Evaluate side-chains 220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 340 ASN ** 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 = 0.3828 r_free = 0.3828 target = 0.140831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126140 restraints weight = 11282.613| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.84 r_work: 0.3530 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8170 Z= 0.189 Angle : 0.580 8.137 11111 Z= 0.309 Chirality : 0.044 0.206 1256 Planarity : 0.004 0.062 1425 Dihedral : 4.597 35.813 1125 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.81 % Allowed : 24.67 % Favored : 70.52 % 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: -0.08 (0.27), residues: 1021 helix: 1.85 (0.27), residues: 382 sheet: -0.82 (0.35), residues: 217 loop : -1.43 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.009 0.001 HIS R 269 PHE 0.021 0.002 PHE R 260 TYR 0.017 0.002 TYR R 76 ARG 0.006 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 384) hydrogen bonds : angle 4.40677 ( 1107) SS BOND : bond 0.00383 ( 2) SS BOND : angle 1.44580 ( 4) covalent geometry : bond 0.00431 ( 8168) covalent geometry : angle 0.57905 (11107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 36 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8432 (p) REVERT: A 271 LYS cc_start: 0.7564 (mmtt) cc_final: 0.7190 (mmtp) REVERT: B 61 MET cc_start: 0.7818 (ppp) cc_final: 0.7223 (ppp) REVERT: B 175 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7805 (mm-40) REVERT: B 176 GLN cc_start: 0.8721 (mt0) cc_final: 0.8397 (mt0) REVERT: B 234 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: B 274 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7921 (m) REVERT: R 23 LEU cc_start: 0.7155 (mp) cc_final: 0.6903 (mp) REVERT: R 83 TRP cc_start: 0.8406 (t-100) cc_final: 0.8131 (t-100) REVERT: R 170 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6869 (pp20) REVERT: R 181 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7161 (tmm) REVERT: R 237 PHE cc_start: 0.7589 (m-10) cc_final: 0.7223 (m-10) outliers start: 40 outliers final: 29 residues processed: 214 average time/residue: 0.2645 time to fit residues: 71.8134 Evaluate side-chains 216 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125353 restraints weight = 11311.331| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.89 r_work: 0.3509 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8170 Z= 0.205 Angle : 0.602 8.036 11111 Z= 0.320 Chirality : 0.044 0.185 1256 Planarity : 0.004 0.062 1425 Dihedral : 4.715 36.607 1125 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.05 % Allowed : 24.43 % Favored : 70.52 % 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: -0.13 (0.26), residues: 1021 helix: 1.81 (0.27), residues: 382 sheet: -0.90 (0.35), residues: 224 loop : -1.42 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 339 HIS 0.009 0.001 HIS R 269 PHE 0.023 0.002 PHE R 260 TYR 0.016 0.002 TYR R 268 ARG 0.005 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 384) hydrogen bonds : angle 4.44681 ( 1107) SS BOND : bond 0.00412 ( 2) SS BOND : angle 1.54742 ( 4) covalent geometry : bond 0.00469 ( 8168) covalent geometry : angle 0.60140 (11107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6769 (tm-30) REVERT: A 36 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8414 (p) REVERT: A 271 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7262 (mmtp) REVERT: A 272 LEU cc_start: 0.7945 (tp) cc_final: 0.7730 (tt) REVERT: B 49 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.7719 (ttm170) REVERT: B 61 MET cc_start: 0.7831 (ppp) cc_final: 0.7324 (ppp) REVERT: B 176 GLN cc_start: 0.8757 (mt0) cc_final: 0.8428 (mt0) REVERT: B 234 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: B 261 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7433 (mp) REVERT: B 274 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7969 (m) REVERT: R 23 LEU cc_start: 0.7186 (mp) cc_final: 0.6931 (mp) REVERT: R 83 TRP cc_start: 0.8417 (t-100) cc_final: 0.8197 (t-100) REVERT: R 170 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6944 (pp20) REVERT: R 181 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7125 (tmm) REVERT: R 237 PHE cc_start: 0.7628 (m-10) cc_final: 0.7205 (m-10) outliers start: 42 outliers final: 30 residues processed: 216 average time/residue: 0.2574 time to fit residues: 70.6978 Evaluate side-chains 217 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 82 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.128006 restraints weight = 11461.165| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.91 r_work: 0.3543 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8170 Z= 0.131 Angle : 0.560 7.862 11111 Z= 0.298 Chirality : 0.042 0.187 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.553 35.764 1125 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.81 % Allowed : 25.75 % Favored : 69.43 % 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: -0.07 (0.27), residues: 1021 helix: 1.92 (0.27), residues: 381 sheet: -0.94 (0.35), residues: 223 loop : -1.40 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.008 0.001 HIS R 269 PHE 0.020 0.002 PHE R 260 TYR 0.025 0.001 TYR R 268 ARG 0.004 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 384) hydrogen bonds : angle 4.35948 ( 1107) SS BOND : bond 0.00194 ( 2) SS BOND : angle 1.05027 ( 4) covalent geometry : bond 0.00289 ( 8168) covalent geometry : angle 0.55978 (11107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6775 (tm-30) REVERT: A 36 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8388 (p) REVERT: A 271 LYS cc_start: 0.7468 (mmtt) cc_final: 0.7188 (mmtp) REVERT: B 61 MET cc_start: 0.7673 (ppp) cc_final: 0.7237 (ppp) REVERT: B 175 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7798 (mm-40) REVERT: B 176 GLN cc_start: 0.8713 (mt0) cc_final: 0.8366 (mt0) REVERT: B 234 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: B 274 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.7951 (m) REVERT: R 83 TRP cc_start: 0.8333 (t-100) cc_final: 0.8099 (t-100) REVERT: R 170 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6867 (pp20) REVERT: R 181 MET cc_start: 0.7826 (mmm) cc_final: 0.7109 (tmm) REVERT: R 237 PHE cc_start: 0.7582 (m-10) cc_final: 0.7176 (m-10) outliers start: 40 outliers final: 31 residues processed: 208 average time/residue: 0.2751 time to fit residues: 72.2918 Evaluate side-chains 214 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** 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 = 0.3844 r_free = 0.3844 target = 0.142400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127719 restraints weight = 11132.350| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.83 r_work: 0.3540 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8170 Z= 0.158 Angle : 0.577 7.914 11111 Z= 0.305 Chirality : 0.043 0.171 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.563 34.644 1125 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.21 % Allowed : 26.23 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.27), residues: 1021 helix: 1.76 (0.27), residues: 386 sheet: -0.98 (0.35), residues: 224 loop : -1.43 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.020 0.002 PHE R 260 TYR 0.023 0.001 TYR R 268 ARG 0.007 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 384) hydrogen bonds : angle 4.37374 ( 1107) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.21040 ( 4) covalent geometry : bond 0.00359 ( 8168) covalent geometry : angle 0.57667 (11107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6768 (tm-30) REVERT: A 36 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 271 LYS cc_start: 0.7500 (mmtt) cc_final: 0.7231 (mmtp) REVERT: B 61 MET cc_start: 0.7676 (ppp) cc_final: 0.7276 (ppp) REVERT: B 175 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7786 (mm-40) REVERT: B 176 GLN cc_start: 0.8712 (mt0) cc_final: 0.8373 (mt0) REVERT: B 234 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: B 274 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7989 (m) REVERT: R 23 LEU cc_start: 0.7496 (tt) cc_final: 0.7283 (tp) REVERT: R 83 TRP cc_start: 0.8362 (t-100) cc_final: 0.8134 (t-100) REVERT: R 170 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6861 (pp20) REVERT: R 181 MET cc_start: 0.7826 (mmm) cc_final: 0.7103 (tmm) REVERT: R 237 PHE cc_start: 0.7580 (m-10) cc_final: 0.7155 (m-10) outliers start: 35 outliers final: 29 residues processed: 202 average time/residue: 0.2824 time to fit residues: 73.2947 Evaluate side-chains 209 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.141968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127241 restraints weight = 11266.876| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.85 r_work: 0.3537 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8170 Z= 0.172 Angle : 0.591 8.245 11111 Z= 0.312 Chirality : 0.044 0.175 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.649 34.336 1125 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.33 % Allowed : 26.23 % Favored : 69.43 % 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: -0.19 (0.27), residues: 1021 helix: 1.68 (0.26), residues: 392 sheet: -1.00 (0.34), residues: 226 loop : -1.41 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.023 0.002 PHE R 260 TYR 0.024 0.002 TYR R 268 ARG 0.007 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04062 ( 384) hydrogen bonds : angle 4.41650 ( 1107) SS BOND : bond 0.00318 ( 2) SS BOND : angle 1.31963 ( 4) covalent geometry : bond 0.00394 ( 8168) covalent geometry : angle 0.59083 (11107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4816.26 seconds wall clock time: 83 minutes 3.56 seconds (4983.56 seconds total)