Starting phenix.real_space_refine on Sun May 11 11:00:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfw_61442/05_2025/9jfw_61442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfw_61442/05_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_61442/05_2025/9jfw_61442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfw_61442/05_2025/9jfw_61442.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfw_61442/05_2025/9jfw_61442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfw_61442/05_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-5687/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: 5.04, 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: 1.83 Conformation dependent library (CDL) restraints added in 1.2 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: 0.82 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: 2.34 Time building geometry restraints manager: 2.18 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: 0.800 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: 21.210 Find NCS groups from input model: 0.140 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- 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 : 0.821 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: 0.2780 time to fit residues: 62.2158 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 : 0.808 ------------------------------------------------------------------------------- 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 = 11374.421| |-----------------------------------------------------------------------------| 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: 0.3428 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- 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 : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 36 VAL cc_start: 0.8687 (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: 0.8614 (mt0) cc_final: 0.8254 (mt0) REVERT: B 243 THR cc_start: 0.7930 (p) cc_final: 0.7724 (p) REVERT: B 261 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7290 (mp) REVERT: N 60 TYR cc_start: 0.7361 (m-80) cc_final: 0.6912 (m-80) REVERT: R 65 LEU cc_start: 0.8183 (mp) cc_final: 0.7963 (mp) REVERT: R 181 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7177 (tmm) REVERT: R 251 TYR cc_start: 0.7999 (t80) cc_final: 0.7479 (t80) outliers start: 40 outliers final: 19 residues processed: 202 average time/residue: 0.2772 time to fit residues: 70.0010 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 : 0.814 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 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 ** 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 = 0.3827 r_free = 0.3827 target = 0.139676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125312 restraints weight = 11420.245| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.73 r_work: 0.3540 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8170 Z= 0.190 Angle : 0.570 7.241 11111 Z= 0.307 Chirality : 0.044 0.166 1256 Planarity : 0.004 0.058 1425 Dihedral : 4.662 40.711 1125 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.33 % Allowed : 22.26 % Favored : 73.41 % 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: 1.70 (0.27), residues: 388 sheet: -0.58 (0.36), residues: 199 loop : -1.53 (0.28), residues: 434 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 0.04370 ( 384) hydrogen bonds : angle 4.48223 ( 1107) SS BOND : bond 0.00311 ( 2) SS BOND : angle 1.39325 ( 4) covalent geometry : bond 0.00431 ( 8168) covalent geometry : angle 0.56967 (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 225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6743 (tm-30) REVERT: A 27 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 49 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7819 (mtt90) REVERT: B 176 GLN cc_start: 0.8639 (mt0) cc_final: 0.8325 (mt0) REVERT: B 205 ASP cc_start: 0.7138 (p0) cc_final: 0.6895 (p0) REVERT: B 234 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: B 243 THR cc_start: 0.7892 (p) cc_final: 0.7690 (p) REVERT: B 274 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7921 (m) REVERT: N 60 TYR cc_start: 0.7434 (m-80) cc_final: 0.7045 (m-80) REVERT: R 65 LEU cc_start: 0.8294 (mp) cc_final: 0.8080 (mp) REVERT: R 170 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6799 (pp20) REVERT: R 181 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7205 (tmm) REVERT: R 251 TYR cc_start: 0.8040 (t80) cc_final: 0.7516 (t80) outliers start: 36 outliers final: 19 residues processed: 209 average time/residue: 0.2533 time to fit residues: 67.2106 Evaluate side-chains 200 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 55 LEU 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 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 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 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: 0.5980 chunk 38 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 340 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 = 0.3828 r_free = 0.3828 target = 0.139985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.125257 restraints weight = 11405.497| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.86 r_work: 0.3536 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8170 Z= 0.161 Angle : 0.554 7.085 11111 Z= 0.296 Chirality : 0.042 0.167 1256 Planarity : 0.004 0.059 1425 Dihedral : 4.540 39.237 1125 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.33 % Allowed : 22.98 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1021 helix: 1.82 (0.27), residues: 383 sheet: -0.58 (0.36), residues: 199 loop : -1.48 (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 R 241 PHE 0.019 0.002 PHE R 19 TYR 0.021 0.001 TYR R 268 ARG 0.004 0.001 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 384) hydrogen bonds : angle 4.38329 ( 1107) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.25938 ( 4) covalent geometry : bond 0.00364 ( 8168) covalent geometry : angle 0.55348 (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 224 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6744 (tm-30) REVERT: A 27 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 36 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 211 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7654 (mmmt) REVERT: A 271 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7360 (mmtp) REVERT: B 176 GLN cc_start: 0.8672 (mt0) cc_final: 0.8323 (mt0) REVERT: B 205 ASP cc_start: 0.7105 (p0) cc_final: 0.6849 (p0) REVERT: B 226 GLU cc_start: 0.7590 (pt0) cc_final: 0.7248 (pt0) REVERT: B 234 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: B 243 THR cc_start: 0.7922 (p) cc_final: 0.7709 (p) REVERT: B 274 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.7900 (m) REVERT: N 60 TYR cc_start: 0.7442 (m-80) cc_final: 0.7111 (m-80) REVERT: R 65 LEU cc_start: 0.8240 (mp) cc_final: 0.8038 (mp) REVERT: R 95 PHE cc_start: 0.8113 (t80) cc_final: 0.7908 (t80) REVERT: R 170 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6771 (pp20) REVERT: R 181 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7135 (tmm) outliers start: 36 outliers final: 19 residues processed: 208 average time/residue: 0.2647 time to fit residues: 69.3804 Evaluate side-chains 202 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 50 THR 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 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 133 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 5 optimal weight: 0.0060 chunk 28 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.141540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126723 restraints weight = 11207.728| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.89 r_work: 0.3542 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2704 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= 0.157 Angle : 0.550 7.615 11111 Z= 0.293 Chirality : 0.042 0.165 1256 Planarity : 0.004 0.062 1425 Dihedral : 4.518 37.108 1125 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.81 % Allowed : 22.26 % Favored : 72.92 % 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: -0.00 (0.26), residues: 1021 helix: 1.86 (0.27), residues: 383 sheet: -0.55 (0.37), residues: 199 loop : -1.45 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.009 0.001 HIS R 269 PHE 0.020 0.002 PHE R 97 TYR 0.018 0.001 TYR R 268 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 384) hydrogen bonds : angle 4.38021 ( 1107) SS BOND : bond 0.00287 ( 2) SS BOND : angle 1.25737 ( 4) covalent geometry : bond 0.00354 ( 8168) covalent geometry : angle 0.55006 (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 225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6726 (tm-30) REVERT: A 36 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8400 (p) REVERT: A 211 LYS cc_start: 0.7859 (mmtp) cc_final: 0.7631 (mmmt) REVERT: A 271 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7331 (mmtp) REVERT: B 176 GLN cc_start: 0.8732 (mt0) cc_final: 0.8441 (mt0) REVERT: B 205 ASP cc_start: 0.7044 (p0) cc_final: 0.6782 (p0) REVERT: B 226 GLU cc_start: 0.7627 (pt0) cc_final: 0.7257 (pt0) REVERT: B 234 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: B 251 ARG cc_start: 0.8329 (mtt90) cc_final: 0.8111 (mtt90) REVERT: B 274 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7893 (m) REVERT: B 293 ASN cc_start: 0.7856 (t0) cc_final: 0.7510 (m-40) REVERT: N 60 TYR cc_start: 0.7532 (m-80) cc_final: 0.7200 (m-80) REVERT: R 95 PHE cc_start: 0.8149 (t80) cc_final: 0.7898 (t80) REVERT: R 170 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6854 (pp20) REVERT: R 181 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7153 (tmm) REVERT: R 237 PHE cc_start: 0.7511 (m-10) cc_final: 0.7085 (m-10) outliers start: 40 outliers final: 26 residues processed: 208 average time/residue: 0.2564 time to fit residues: 67.2642 Evaluate side-chains 210 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 280 LYS 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 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 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 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 R residue 125 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.0020 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 0.0370 overall best weight: 0.2244 ------------------------------------------------------------------------------- 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** 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 = 0.3875 r_free = 0.3875 target = 0.144788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129975 restraints weight = 11206.294| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.89 r_work: 0.3575 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8170 Z= 0.110 Angle : 0.521 7.741 11111 Z= 0.279 Chirality : 0.041 0.159 1256 Planarity : 0.005 0.063 1425 Dihedral : 4.327 36.095 1125 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.21 % Allowed : 24.55 % 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: 0.10 (0.27), residues: 1021 helix: 2.04 (0.27), residues: 382 sheet: -0.56 (0.37), residues: 201 loop : -1.44 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.006 0.001 HIS R 269 PHE 0.017 0.002 PHE R 260 TYR 0.017 0.001 TYR R 268 ARG 0.011 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 384) hydrogen bonds : angle 4.24492 ( 1107) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.94209 ( 4) covalent geometry : bond 0.00233 ( 8168) covalent geometry : angle 0.52111 (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 233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6714 (tm-30) REVERT: A 36 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8313 (p) REVERT: A 211 LYS cc_start: 0.7880 (mmtp) cc_final: 0.7608 (mmmt) REVERT: A 272 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7755 (tp) REVERT: B 38 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7737 (t0) REVERT: B 61 MET cc_start: 0.7860 (ppp) cc_final: 0.7355 (ppp) REVERT: B 176 GLN cc_start: 0.8708 (mt0) cc_final: 0.8387 (mt0) REVERT: B 205 ASP cc_start: 0.6962 (p0) cc_final: 0.6691 (p0) REVERT: B 234 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: B 274 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7917 (m) REVERT: N 60 TYR cc_start: 0.7398 (m-80) cc_final: 0.7042 (m-80) REVERT: R 95 PHE cc_start: 0.8160 (t80) cc_final: 0.7879 (t80) REVERT: R 170 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6799 (pp20) REVERT: R 181 MET cc_start: 0.7799 (mmm) cc_final: 0.7100 (tmm) outliers start: 35 outliers final: 19 residues processed: 218 average time/residue: 0.2519 time to fit residues: 69.6522 Evaluate side-chains 210 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 272 LEU Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 357 HIS 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 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 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 108 PHE Chi-restraints excluded: chain R residue 125 PHE 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: 0.8980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 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 239 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 = 0.3834 r_free = 0.3834 target = 0.141548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126662 restraints weight = 11325.744| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.89 r_work: 0.3530 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8170 Z= 0.189 Angle : 0.583 7.481 11111 Z= 0.309 Chirality : 0.043 0.195 1256 Planarity : 0.004 0.062 1425 Dihedral : 4.524 35.432 1125 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.45 % Allowed : 25.15 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 1021 helix: 1.82 (0.27), residues: 387 sheet: -0.58 (0.37), residues: 203 loop : -1.49 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 83 HIS 0.008 0.001 HIS R 269 PHE 0.021 0.002 PHE R 97 TYR 0.016 0.002 TYR R 76 ARG 0.007 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 384) hydrogen bonds : angle 4.38973 ( 1107) SS BOND : bond 0.00364 ( 2) SS BOND : angle 1.36628 ( 4) covalent geometry : bond 0.00432 ( 8168) covalent geometry : angle 0.58207 (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 219 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6733 (tm-30) REVERT: A 36 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8417 (p) REVERT: A 211 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7596 (mmmt) REVERT: A 271 LYS cc_start: 0.7640 (mmtt) cc_final: 0.7202 (mmtp) REVERT: B 61 MET cc_start: 0.7894 (ppp) cc_final: 0.7313 (ppp) REVERT: B 176 GLN cc_start: 0.8714 (mt0) cc_final: 0.8400 (mt0) REVERT: B 234 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: B 274 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7949 (m) REVERT: R 95 PHE cc_start: 0.8163 (t80) cc_final: 0.7871 (t80) REVERT: R 170 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: R 181 MET cc_start: 0.7893 (mmm) cc_final: 0.7127 (tmm) REVERT: R 237 PHE cc_start: 0.7602 (m-10) cc_final: 0.7214 (m-10) outliers start: 37 outliers final: 25 residues processed: 206 average time/residue: 0.2626 time to fit residues: 68.0219 Evaluate side-chains 207 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 272 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 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3838 r_free = 0.3838 target = 0.141871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127159 restraints weight = 11293.304| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.84 r_work: 0.3537 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8170 Z= 0.163 Angle : 0.571 8.132 11111 Z= 0.303 Chirality : 0.043 0.167 1256 Planarity : 0.005 0.111 1425 Dihedral : 4.552 35.573 1125 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.21 % Allowed : 25.27 % 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 (0.27), residues: 1021 helix: 1.76 (0.27), residues: 387 sheet: -0.88 (0.35), residues: 226 loop : -1.41 (0.29), residues: 408 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 R 260 TYR 0.016 0.001 TYR R 268 ARG 0.019 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 384) hydrogen bonds : angle 4.37910 ( 1107) SS BOND : bond 0.00303 ( 2) SS BOND : angle 1.25282 ( 4) covalent geometry : bond 0.00371 ( 8168) covalent geometry : angle 0.57082 (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 214 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 36 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8418 (p) REVERT: A 211 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7601 (mmmt) REVERT: A 271 LYS cc_start: 0.7598 (mmtt) cc_final: 0.7267 (mmtp) REVERT: B 61 MET cc_start: 0.7839 (ppp) cc_final: 0.7360 (ppp) REVERT: B 176 GLN cc_start: 0.8714 (mt0) cc_final: 0.8402 (mt0) REVERT: B 234 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: B 274 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7946 (m) REVERT: R 95 PHE cc_start: 0.8143 (t80) cc_final: 0.7858 (t80) REVERT: R 170 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6859 (pp20) REVERT: R 181 MET cc_start: 0.7826 (mmm) cc_final: 0.7109 (tmm) outliers start: 35 outliers final: 28 residues processed: 201 average time/residue: 0.2728 time to fit residues: 69.0054 Evaluate side-chains 207 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 93 ILE 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 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 339 TRP 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3836 r_free = 0.3836 target = 0.141688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126778 restraints weight = 11481.891| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.91 r_work: 0.3527 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3190 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= 0.157 Angle : 0.575 8.071 11111 Z= 0.304 Chirality : 0.043 0.171 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.536 35.012 1125 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.21 % Allowed : 25.39 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.27), residues: 1021 helix: 1.74 (0.27), residues: 387 sheet: -0.73 (0.35), residues: 216 loop : -1.50 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.007 0.001 HIS R 269 PHE 0.020 0.002 PHE R 260 TYR 0.016 0.001 TYR R 268 ARG 0.007 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 384) hydrogen bonds : angle 4.37515 ( 1107) SS BOND : bond 0.00296 ( 2) SS BOND : angle 1.22954 ( 4) covalent geometry : bond 0.00357 ( 8168) covalent geometry : angle 0.57455 (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 216 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6801 (tm-30) REVERT: A 36 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (p) REVERT: A 211 LYS cc_start: 0.7867 (mmtp) cc_final: 0.7593 (mmmt) REVERT: A 271 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7251 (mmtp) REVERT: B 61 MET cc_start: 0.7753 (ppp) cc_final: 0.7306 (ppp) REVERT: B 176 GLN cc_start: 0.8712 (mt0) cc_final: 0.8386 (mt0) REVERT: B 234 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: B 274 THR cc_start: 0.8293 (OUTLIER) cc_final: 0.7964 (m) REVERT: R 95 PHE cc_start: 0.8145 (t80) cc_final: 0.7867 (t80) REVERT: R 170 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6871 (pp20) REVERT: R 181 MET cc_start: 0.7829 (mmm) cc_final: 0.7104 (tmm) REVERT: R 237 PHE cc_start: 0.7510 (m-10) cc_final: 0.7142 (m-10) outliers start: 35 outliers final: 30 residues processed: 203 average time/residue: 0.2697 time to fit residues: 68.9818 Evaluate side-chains 210 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 258 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 339 TRP 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 18 LEU Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 125 PHE 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: 0.8980 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 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 A 292 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125616 restraints weight = 11191.148| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.83 r_work: 0.3522 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3324 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 : 0.599 8.143 11111 Z= 0.316 Chirality : 0.044 0.168 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.685 35.460 1125 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.33 % Allowed : 25.03 % Favored : 70.64 % 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: -0.27 (0.26), residues: 1021 helix: 1.62 (0.26), residues: 386 sheet: -0.99 (0.35), residues: 226 loop : -1.45 (0.29), residues: 409 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 0.023 0.002 PHE R 260 TYR 0.016 0.002 TYR R 76 ARG 0.008 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 384) hydrogen bonds : angle 4.44667 ( 1107) SS BOND : bond 0.00370 ( 2) SS BOND : angle 1.39871 ( 4) covalent geometry : bond 0.00433 ( 8168) covalent geometry : angle 0.59896 (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 219 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6811 (tm-30) REVERT: A 36 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8428 (p) REVERT: A 211 LYS cc_start: 0.7867 (mmtp) cc_final: 0.7602 (mmmt) REVERT: A 271 LYS cc_start: 0.7555 (mmtt) cc_final: 0.7307 (mmtp) REVERT: B 61 MET cc_start: 0.7756 (ppp) cc_final: 0.7311 (ppp) REVERT: B 176 GLN cc_start: 0.8707 (mt0) cc_final: 0.8402 (mt0) REVERT: B 234 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: B 274 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7951 (m) REVERT: R 95 PHE cc_start: 0.8122 (t80) cc_final: 0.7847 (t80) REVERT: R 170 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: R 181 MET cc_start: 0.7821 (mmm) cc_final: 0.7099 (tmm) REVERT: R 237 PHE cc_start: 0.7549 (m-10) cc_final: 0.7195 (m-10) outliers start: 36 outliers final: 27 residues processed: 205 average time/residue: 0.2686 time to fit residues: 69.4571 Evaluate side-chains 207 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 272 LEU 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 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 258 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS 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 108 PHE Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 125 PHE 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: 0.7980 chunk 83 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3840 r_free = 0.3840 target = 0.141933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127346 restraints weight = 11317.847| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.84 r_work: 0.3544 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.150 Angle : 0.585 7.956 11111 Z= 0.309 Chirality : 0.043 0.176 1256 Planarity : 0.005 0.092 1425 Dihedral : 4.649 34.938 1125 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.85 % Allowed : 26.11 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 1021 helix: 1.71 (0.27), residues: 387 sheet: -0.83 (0.36), residues: 209 loop : -1.45 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS R 269 PHE 0.021 0.002 PHE R 260 TYR 0.024 0.001 TYR R 268 ARG 0.012 0.001 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 384) hydrogen bonds : angle 4.39453 ( 1107) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.15637 ( 4) covalent geometry : bond 0.00342 ( 8168) covalent geometry : angle 0.58423 (11107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.22 seconds wall clock time: 75 minutes 43.41 seconds (4543.41 seconds total)