Starting phenix.real_space_refine on Wed Sep 17 10:07:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfw_61442/09_2025/9jfw_61442.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfw_61442/09_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_61442/09_2025/9jfw_61442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfw_61442/09_2025/9jfw_61442.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfw_61442/09_2025/9jfw_61442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfw_61442/09_2025/9jfw_61442.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ARG:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} 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: {'GLU:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 5, 'ASN:plan1': 1} 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: {'ARG:plan': 6, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 1.98, per 1000 atoms: 0.25 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: 0.68 Conformation dependent library (CDL) restraints added in 418.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.29 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: 1.25 Time building geometry restraints manager: 0.91 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.830 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.580 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG N 19 TYR 0.012 0.001 TYR R 268 PHE 0.018 0.002 PHE R 172 TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8168) covalent geometry : angle 0.61931 (11107) SS BOND : bond 0.00175 ( 2) SS BOND : angle 1.02051 ( 4) hydrogen bonds : bond 0.14647 ( 384) hydrogen bonds : angle 6.11022 ( 1107) *********************** 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 : 0.297 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: 0.1291 time to fit residues: 28.9649 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 : 0.288 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 220 HIS A 294 GLN A 371 ASN B 88 ASN R 165 HIS R 269 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.143017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.128535 restraints weight = 11512.597| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.75 r_work: 0.3589 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8170 Z= 0.147 Angle : 0.547 6.734 11111 Z= 0.296 Chirality : 0.042 0.165 1256 Planarity : 0.004 0.041 1425 Dihedral : 4.999 59.495 1127 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.21 % Allowed : 23.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1021 helix: 1.80 (0.27), residues: 386 sheet: -0.85 (0.35), residues: 217 loop : -1.48 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 209 TYR 0.017 0.002 TYR R 268 PHE 0.019 0.002 PHE R 97 TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8168) covalent geometry : angle 0.54712 (11107) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.19533 ( 4) hydrogen bonds : bond 0.04060 ( 384) hydrogen bonds : angle 4.57244 ( 1107) *********************** 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: 35 poor density : 185 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6704 (tm-30) REVERT: A 36 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8457 (p) REVERT: A 231 ARG cc_start: 0.8281 (mtt90) cc_final: 0.8013 (mtt90) REVERT: B 49 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7988 (ttm-80) REVERT: B 175 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7742 (mm-40) REVERT: B 176 GLN cc_start: 0.8586 (mt0) cc_final: 0.8266 (mt0) REVERT: N 60 TYR cc_start: 0.7347 (m-80) cc_final: 0.6909 (m-80) REVERT: R 23 LEU cc_start: 0.7035 (mp) cc_final: 0.6569 (mp) REVERT: R 65 LEU cc_start: 0.8168 (mp) cc_final: 0.7926 (mp) REVERT: R 181 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7157 (tmm) REVERT: R 209 ARG cc_start: 0.8261 (ttp80) cc_final: 0.8018 (ttp80) REVERT: R 251 TYR cc_start: 0.7948 (t80) cc_final: 0.7408 (t80) outliers start: 35 outliers final: 14 residues processed: 204 average time/residue: 0.1279 time to fit residues: 32.6583 Evaluate side-chains 194 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 142 HIS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.125562 restraints weight = 11370.036| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.72 r_work: 0.3553 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8170 Z= 0.181 Angle : 0.560 7.096 11111 Z= 0.301 Chirality : 0.043 0.167 1256 Planarity : 0.004 0.058 1425 Dihedral : 4.590 42.493 1125 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.09 % Allowed : 22.86 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1021 helix: 1.74 (0.27), residues: 389 sheet: -0.65 (0.36), residues: 201 loop : -1.48 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 72 TYR 0.021 0.002 TYR R 268 PHE 0.024 0.002 PHE R 97 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8168) covalent geometry : angle 0.55972 (11107) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.29793 ( 4) hydrogen bonds : bond 0.04266 ( 384) hydrogen bonds : angle 4.44731 ( 1107) *********************** 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 218 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6733 (tm-30) REVERT: B 175 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7717 (mm-40) REVERT: B 176 GLN cc_start: 0.8627 (mt0) cc_final: 0.8297 (mt0) REVERT: B 234 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: B 261 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7386 (mp) REVERT: B 274 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7881 (m) REVERT: N 60 TYR cc_start: 0.7382 (m-80) cc_final: 0.6912 (m-80) REVERT: R 23 LEU cc_start: 0.7091 (mp) cc_final: 0.6610 (mp) REVERT: R 65 LEU cc_start: 0.8249 (mp) cc_final: 0.8035 (mp) REVERT: R 170 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6751 (pp20) REVERT: R 181 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7222 (tmm) REVERT: R 237 PHE cc_start: 0.7492 (m-10) cc_final: 0.7104 (m-10) REVERT: R 251 TYR cc_start: 0.8014 (t80) cc_final: 0.7526 (t80) outliers start: 34 outliers final: 17 residues processed: 201 average time/residue: 0.1280 time to fit residues: 32.4596 Evaluate side-chains 198 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN 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 357 HIS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 0.0050 chunk 33 optimal weight: 0.7980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127171 restraints weight = 11623.506| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.77 r_work: 0.3567 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8170 Z= 0.136 Angle : 0.532 7.139 11111 Z= 0.285 Chirality : 0.042 0.334 1256 Planarity : 0.004 0.059 1425 Dihedral : 4.445 39.979 1125 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.81 % Allowed : 22.38 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.27), residues: 1021 helix: 1.89 (0.27), residues: 388 sheet: -0.55 (0.36), residues: 199 loop : -1.46 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 98 TYR 0.020 0.001 TYR R 268 PHE 0.023 0.002 PHE R 97 TRP 0.012 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8168) covalent geometry : angle 0.53216 (11107) SS BOND : bond 0.00191 ( 2) SS BOND : angle 1.05641 ( 4) hydrogen bonds : bond 0.03771 ( 384) hydrogen bonds : angle 4.29677 ( 1107) *********************** 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 231 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 36 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8469 (p) REVERT: A 271 LYS cc_start: 0.7553 (mmtt) cc_final: 0.7109 (mmtt) REVERT: B 163 ASP cc_start: 0.7514 (p0) cc_final: 0.7303 (p0) REVERT: B 176 GLN cc_start: 0.8617 (mt0) cc_final: 0.8291 (mt0) REVERT: B 226 GLU cc_start: 0.7562 (pt0) cc_final: 0.7261 (pt0) REVERT: B 234 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: B 261 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7318 (mp) REVERT: B 274 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7837 (m) REVERT: N 60 TYR cc_start: 0.7306 (m-80) cc_final: 0.6910 (m-80) REVERT: R 23 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6769 (mp) REVERT: R 65 LEU cc_start: 0.8326 (mp) cc_final: 0.8113 (mp) REVERT: R 170 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6682 (pp20) REVERT: R 181 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7210 (tmm) outliers start: 40 outliers final: 18 residues processed: 212 average time/residue: 0.1279 time to fit residues: 34.2707 Evaluate side-chains 201 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 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 = 0.3817 r_free = 0.3817 target = 0.139182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124855 restraints weight = 11610.652| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.75 r_work: 0.3537 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2740 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= 0.190 Angle : 0.584 7.138 11111 Z= 0.311 Chirality : 0.044 0.230 1256 Planarity : 0.004 0.062 1425 Dihedral : 4.631 37.673 1125 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.93 % Allowed : 22.62 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1021 helix: 1.73 (0.27), residues: 388 sheet: -0.61 (0.36), residues: 202 loop : -1.47 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 98 TYR 0.018 0.002 TYR R 76 PHE 0.027 0.002 PHE R 97 TRP 0.013 0.002 TRP B 211 HIS 0.006 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8168) covalent geometry : angle 0.58392 (11107) SS BOND : bond 0.00358 ( 2) SS BOND : angle 1.44763 ( 4) hydrogen bonds : bond 0.04286 ( 384) hydrogen bonds : angle 4.43560 ( 1107) *********************** 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 223 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6776 (tm-30) REVERT: A 36 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8481 (p) REVERT: A 270 LEU cc_start: 0.7480 (mt) cc_final: 0.7275 (mt) REVERT: A 271 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7394 (mmtp) REVERT: B 176 GLN cc_start: 0.8647 (mt0) cc_final: 0.8335 (mt0) REVERT: B 234 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: B 261 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7443 (mp) REVERT: B 274 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7911 (m) REVERT: N 60 TYR cc_start: 0.7518 (m-80) cc_final: 0.7143 (m-80) REVERT: R 23 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6858 (mp) REVERT: R 170 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: R 181 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7179 (tmm) outliers start: 41 outliers final: 24 residues processed: 207 average time/residue: 0.1315 time to fit residues: 34.2733 Evaluate side-chains 205 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 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 56 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 4 optimal weight: 0.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126529 restraints weight = 11302.253| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.90 r_work: 0.3528 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2882 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= 0.165 Angle : 0.564 7.908 11111 Z= 0.299 Chirality : 0.043 0.168 1256 Planarity : 0.005 0.078 1425 Dihedral : 4.583 36.856 1125 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.05 % Allowed : 23.59 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1021 helix: 1.81 (0.27), residues: 387 sheet: -0.60 (0.36), residues: 201 loop : -1.50 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 219 TYR 0.017 0.001 TYR R 268 PHE 0.025 0.002 PHE R 97 TRP 0.012 0.002 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8168) covalent geometry : angle 0.56319 (11107) SS BOND : bond 0.00307 ( 2) SS BOND : angle 1.30088 ( 4) hydrogen bonds : bond 0.04011 ( 384) hydrogen bonds : angle 4.38450 ( 1107) *********************** 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 226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6753 (tm-30) REVERT: A 36 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (p) REVERT: B 176 GLN cc_start: 0.8725 (mt0) cc_final: 0.8417 (mt0) REVERT: B 212 ASP cc_start: 0.6842 (p0) cc_final: 0.6591 (p0) REVERT: B 219 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: B 226 GLU cc_start: 0.7649 (pt0) cc_final: 0.7419 (pt0) REVERT: B 234 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: B 261 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7443 (mp) REVERT: B 274 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.7924 (m) REVERT: B 293 ASN cc_start: 0.7876 (t0) cc_final: 0.7505 (m-40) REVERT: N 60 TYR cc_start: 0.7591 (m-80) cc_final: 0.7194 (m-80) REVERT: R 23 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6855 (mp) REVERT: R 170 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: R 181 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7150 (tmm) REVERT: R 237 PHE cc_start: 0.7538 (m-10) cc_final: 0.7133 (m-10) outliers start: 42 outliers final: 31 residues processed: 208 average time/residue: 0.1215 time to fit residues: 32.0389 Evaluate side-chains 214 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 67 SER 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 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 0.0670 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN R 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127655 restraints weight = 11283.470| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.84 r_work: 0.3541 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8170 Z= 0.142 Angle : 0.556 8.150 11111 Z= 0.297 Chirality : 0.042 0.202 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.518 35.899 1125 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.54 % Allowed : 23.71 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.27), residues: 1021 helix: 1.85 (0.27), residues: 387 sheet: -0.63 (0.37), residues: 201 loop : -1.47 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 44 TYR 0.016 0.001 TYR R 268 PHE 0.025 0.002 PHE R 97 TRP 0.011 0.002 TRP A 234 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8168) covalent geometry : angle 0.55523 (11107) SS BOND : bond 0.00242 ( 2) SS BOND : angle 1.15554 ( 4) hydrogen bonds : bond 0.03847 ( 384) hydrogen bonds : angle 4.36234 ( 1107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 36 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (p) REVERT: A 271 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7013 (mmtt) REVERT: B 176 GLN cc_start: 0.8695 (mt0) cc_final: 0.8388 (mt0) REVERT: B 226 GLU cc_start: 0.7618 (pt0) cc_final: 0.7391 (pt0) REVERT: B 234 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: B 261 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7366 (mp) REVERT: B 274 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7942 (m) REVERT: N 60 TYR cc_start: 0.7435 (m-80) cc_final: 0.7052 (m-80) REVERT: R 95 PHE cc_start: 0.8074 (t80) cc_final: 0.7770 (t80) REVERT: R 170 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6866 (pp20) REVERT: R 181 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7131 (tmm) outliers start: 46 outliers final: 33 residues processed: 214 average time/residue: 0.1261 time to fit residues: 34.2150 Evaluate side-chains 218 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 334 VAL 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 67 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain N residue 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 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3823 r_free = 0.3823 target = 0.140807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126051 restraints weight = 11270.304| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.85 r_work: 0.3523 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3153 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= 0.182 Angle : 0.593 8.024 11111 Z= 0.314 Chirality : 0.043 0.176 1256 Planarity : 0.004 0.062 1425 Dihedral : 4.636 36.116 1125 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.93 % Allowed : 24.31 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.26), residues: 1021 helix: 1.75 (0.27), residues: 385 sheet: -0.63 (0.36), residues: 202 loop : -1.48 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 68 TYR 0.015 0.002 TYR R 76 PHE 0.025 0.002 PHE R 97 TRP 0.013 0.002 TRP R 83 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8168) covalent geometry : angle 0.59302 (11107) SS BOND : bond 0.00319 ( 2) SS BOND : angle 1.35142 ( 4) hydrogen bonds : bond 0.04095 ( 384) hydrogen bonds : angle 4.41763 ( 1107) *********************** 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 225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6752 (tm-30) REVERT: A 28 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7735 (mtmt) REVERT: A 36 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 271 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7186 (mmtt) REVERT: B 176 GLN cc_start: 0.8730 (mt0) cc_final: 0.8401 (mt0) REVERT: B 214 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7720 (mtt90) REVERT: B 234 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: B 274 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7949 (m) REVERT: N 60 TYR cc_start: 0.7577 (m-80) cc_final: 0.7207 (m-80) REVERT: R 23 LEU cc_start: 0.7537 (tt) cc_final: 0.7306 (tp) REVERT: R 95 PHE cc_start: 0.8122 (t80) cc_final: 0.7779 (t80) REVERT: R 170 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: R 181 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7123 (tmm) REVERT: R 237 PHE cc_start: 0.7555 (m-10) cc_final: 0.7220 (m-10) outliers start: 41 outliers final: 32 residues processed: 207 average time/residue: 0.1217 time to fit residues: 31.9875 Evaluate side-chains 216 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 280 LYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain 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 65 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.141609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126893 restraints weight = 11281.286| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.84 r_work: 0.3537 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8170 Z= 0.151 Angle : 0.575 8.184 11111 Z= 0.305 Chirality : 0.043 0.176 1256 Planarity : 0.004 0.061 1425 Dihedral : 4.590 35.699 1125 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.29 % Allowed : 24.55 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.26), residues: 1021 helix: 1.83 (0.27), residues: 385 sheet: -0.54 (0.37), residues: 196 loop : -1.46 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 68 TYR 0.024 0.001 TYR R 268 PHE 0.024 0.002 PHE R 97 TRP 0.011 0.002 TRP B 169 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8168) covalent geometry : angle 0.57428 (11107) SS BOND : bond 0.00256 ( 2) SS BOND : angle 1.16321 ( 4) hydrogen bonds : bond 0.03872 ( 384) hydrogen bonds : angle 4.37884 ( 1107) *********************** 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 221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6750 (tm-30) REVERT: A 36 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8419 (p) REVERT: A 271 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7169 (mmtt) REVERT: B 175 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7728 (mm-40) REVERT: B 176 GLN cc_start: 0.8708 (mt0) cc_final: 0.8376 (mt0) REVERT: B 214 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7578 (mtt90) REVERT: B 234 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 274 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.7956 (m) REVERT: R 95 PHE cc_start: 0.8102 (t80) cc_final: 0.7768 (t80) REVERT: R 170 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6822 (pp20) REVERT: R 181 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: R 237 PHE cc_start: 0.7566 (m-10) cc_final: 0.7203 (m-10) outliers start: 44 outliers final: 35 residues processed: 204 average time/residue: 0.1189 time to fit residues: 30.9703 Evaluate side-chains 215 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain 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 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 0.5980 chunk 86 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 0.0570 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 overall best weight: 0.3912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN B 36 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127788 restraints weight = 11306.784| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.84 r_work: 0.3552 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8170 Z= 0.129 Angle : 0.564 8.152 11111 Z= 0.299 Chirality : 0.042 0.172 1256 Planarity : 0.004 0.067 1425 Dihedral : 4.507 34.565 1125 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.69 % Allowed : 25.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.27), residues: 1021 helix: 1.82 (0.27), residues: 387 sheet: -0.80 (0.36), residues: 207 loop : -1.40 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 374 TYR 0.023 0.001 TYR R 268 PHE 0.025 0.002 PHE R 97 TRP 0.012 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8168) covalent geometry : angle 0.56332 (11107) SS BOND : bond 0.00161 ( 2) SS BOND : angle 0.96738 ( 4) hydrogen bonds : bond 0.03658 ( 384) hydrogen bonds : angle 4.32365 ( 1107) ********************** 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 220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6661 (tm-30) REVERT: A 28 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7718 (mtmt) REVERT: A 36 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8332 (p) REVERT: A 271 LYS cc_start: 0.7497 (mmtt) cc_final: 0.7067 (mmtt) REVERT: B 175 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7669 (mm-40) REVERT: B 176 GLN cc_start: 0.8690 (mt0) cc_final: 0.8350 (mt0) REVERT: B 214 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7480 (mtt90) REVERT: B 234 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: B 251 ARG cc_start: 0.8255 (mtt90) cc_final: 0.8023 (mtt90) REVERT: B 274 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7917 (m) REVERT: C 13 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7494 (mtm-85) REVERT: R 95 PHE cc_start: 0.8117 (t80) cc_final: 0.7779 (t80) REVERT: R 170 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6789 (pp20) REVERT: R 181 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7106 (tmm) outliers start: 39 outliers final: 29 residues processed: 204 average time/residue: 0.1095 time to fit residues: 28.6627 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 : 0.233 ------------------------------------------------------------------------------- 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 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 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 339 TRP 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 18 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 125 PHE Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.0010 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 156 GLN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.142354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127622 restraints weight = 11254.110| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.85 r_work: 0.3549 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8170 Z= 0.144 Angle : 0.586 9.449 11111 Z= 0.308 Chirality : 0.043 0.176 1256 Planarity : 0.005 0.112 1425 Dihedral : 4.568 33.880 1125 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.57 % Allowed : 25.51 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.27), residues: 1021 helix: 1.78 (0.27), residues: 387 sheet: -0.79 (0.36), residues: 207 loop : -1.41 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 374 TYR 0.021 0.001 TYR R 268 PHE 0.024 0.002 PHE R 97 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8168) covalent geometry : angle 0.58538 (11107) SS BOND : bond 0.00273 ( 2) SS BOND : angle 1.06588 ( 4) hydrogen bonds : bond 0.03741 ( 384) hydrogen bonds : angle 4.35043 ( 1107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.89 seconds wall clock time: 40 minutes 18.17 seconds (2418.17 seconds total)