Starting phenix.real_space_refine on Wed Sep 17 08:36:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x9b_33070/09_2025/7x9b_33070.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x9b_33070/09_2025/7x9b_33070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x9b_33070/09_2025/7x9b_33070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x9b_33070/09_2025/7x9b_33070.map" model { file = "/net/cci-nas-00/data/ceres_data/7x9b_33070/09_2025/7x9b_33070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x9b_33070/09_2025/7x9b_33070.cif" } resolution = 3.4 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= 0.003 sd= 0.053 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 45 5.16 5 C 4634 2.51 5 N 1242 2.21 5 O 1321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 7242 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1684 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2523 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 391 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2362 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 291} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 282 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 1.94, per 1000 atoms: 0.27 Number of scatterers: 7242 At special positions: 0 Unit cell: (111.52, 125.46, 84.46, 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 45 16.00 O 1321 8.00 N 1242 7.00 C 4634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 203 " 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: 0.62 Conformation dependent library (CDL) restraints added in 431.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 44.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 7 through 33 removed outlier: 4.226A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.763A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.461A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.609A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.623A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.636A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.048A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.740A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.796A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 4.420A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 37 removed outlier: 3.703A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 37 " --> pdb=" O THR B 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 37' Processing helix chain 'C' and resid 10 through 24 removed outlier: 4.291A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.611A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 78 Processing helix chain 'R' and resid 83 through 104 removed outlier: 4.285A pdb=" N LEU R 104 " --> pdb=" O ASN R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 112 removed outlier: 3.882A pdb=" N TYR R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 124 Processing helix chain 'R' and resid 125 through 153 Processing helix chain 'R' and resid 161 through 180 Processing helix chain 'R' and resid 181 through 184 Processing helix chain 'R' and resid 213 through 249 Proline residue: R 231 - end of helix Processing helix chain 'R' and resid 259 through 294 removed outlier: 3.648A pdb=" N PHE R 277 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA R 278 " --> pdb=" O VAL R 274 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 328 removed outlier: 4.474A pdb=" N SER R 317 " --> pdb=" O ILE R 313 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE R 319 " --> pdb=" O MET R 315 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 329 through 340 removed outlier: 3.764A pdb=" N LEU R 337 " --> pdb=" O ARG R 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.697A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.090A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.374A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 112 removed outlier: 5.833A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.741A 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 149 removed outlier: 6.776A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.755A 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: 6.651A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.635A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.785A 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: 3.811A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.580A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 963 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: 1.12 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2338 1.34 - 1.46: 1525 1.46 - 1.58: 3466 1.58 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7391 Sorted by residual: bond pdb=" CB TYC P 36 " pdb=" CG TYC P 36 " ideal model delta sigma weight residual 1.501 1.389 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C LEU R 230 " pdb=" N PRO R 231 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.30e-02 5.92e+03 1.60e+00 bond pdb=" N TYC P 36 " pdb=" CA TYC P 36 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.90e-02 2.77e+03 1.17e+00 bond pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 1.460 1.473 -0.014 1.54e-02 4.22e+03 7.97e-01 bond pdb=" C LYS P 4 " pdb=" N PRO P 5 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.42e-01 ... (remaining 7386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 9889 1.54 - 3.07: 121 3.07 - 4.61: 21 4.61 - 6.15: 17 6.15 - 7.68: 2 Bond angle restraints: 10050 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.50 3.70 9.60e-01 1.09e+00 1.48e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" CB THR B 164 " ideal model delta sigma weight residual 113.65 109.47 4.18 1.47e+00 4.63e-01 8.07e+00 angle pdb=" C GLU R 210 " pdb=" N GLU R 211 " pdb=" CA GLU R 211 " ideal model delta sigma weight residual 121.54 126.72 -5.18 1.91e+00 2.74e-01 7.37e+00 angle pdb=" CA LEU R 55 " pdb=" CB LEU R 55 " pdb=" CG LEU R 55 " ideal model delta sigma weight residual 116.30 123.98 -7.68 3.50e+00 8.16e-02 4.82e+00 angle pdb=" N ALA R 202 " pdb=" CA ALA R 202 " pdb=" C ALA R 202 " ideal model delta sigma weight residual 108.46 111.51 -3.05 1.51e+00 4.39e-01 4.08e+00 ... (remaining 10045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4054 17.96 - 35.92: 261 35.92 - 53.88: 49 53.88 - 71.84: 8 71.84 - 89.80: 2 Dihedral angle restraints: 4374 sinusoidal: 1609 harmonic: 2765 Sorted by residual: dihedral pdb=" CB CYS R 123 " pdb=" SG CYS R 123 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual -86.00 -153.21 67.21 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " pdb=" CG ASP B 298 " pdb=" OD1 ASP B 298 " ideal model delta sinusoidal sigma weight residual -30.00 -88.31 58.31 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA SER A 326 " pdb=" C SER A 326 " pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta harmonic sigma weight residual 180.00 -164.58 -15.42 0 5.00e+00 4.00e-02 9.51e+00 ... (remaining 4371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 691 0.027 - 0.054: 310 0.054 - 0.081: 108 0.081 - 0.109: 54 0.109 - 0.136: 20 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CB ILE R 66 " pdb=" CA ILE R 66 " pdb=" CG1 ILE R 66 " pdb=" CG2 ILE R 66 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE R 194 " pdb=" N ILE R 194 " pdb=" C ILE R 194 " pdb=" CB ILE R 194 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1180 not shown) Planarity restraints: 1262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 4 " 0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO P 5 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO P 5 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO P 5 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 226 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ILE R 226 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE R 226 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 227 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 238 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C SER R 238 " -0.022 2.00e-02 2.50e+03 pdb=" O SER R 238 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR R 239 " 0.008 2.00e-02 2.50e+03 ... (remaining 1259 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2110 2.81 - 3.33: 6960 3.33 - 3.85: 12021 3.85 - 4.38: 13502 4.38 - 4.90: 23546 Nonbonded interactions: 58139 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" OE2 GLU A 298 " model vdw 2.284 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.289 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP A 341 " pdb=" NE2 HIS R 249 " model vdw 2.323 3.120 nonbonded pdb=" O ARG P 25 " pdb=" ND2 ASN P 29 " model vdw 2.324 3.120 ... (remaining 58134 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.540 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.002 0.112 7392 Z= 0.115 Angle : 0.510 7.682 10052 Z= 0.275 Chirality : 0.040 0.136 1183 Planarity : 0.003 0.064 1262 Dihedral : 12.290 89.805 2577 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % 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: -3.52 (0.23), residues: 931 helix: -0.99 (0.23), residues: 398 sheet: -3.11 (0.39), residues: 137 loop : -3.48 (0.23), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 27 TYR 0.005 0.001 TYR R 228 PHE 0.010 0.001 PHE R 340 TRP 0.004 0.000 TRP B 82 HIS 0.002 0.000 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7391) covalent geometry : angle 0.51032 (10050) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.44624 ( 2) hydrogen bonds : bond 0.17562 ( 337) hydrogen bonds : angle 6.75388 ( 963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 25 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 33 GLU cc_start: 0.9020 (pp20) cc_final: 0.8485 (pp20) REVERT: A 191 PHE cc_start: 0.8324 (t80) cc_final: 0.8011 (t80) REVERT: A 195 HIS cc_start: 0.8167 (m-70) cc_final: 0.7646 (m-70) REVERT: A 224 CYS cc_start: 0.7098 (t) cc_final: 0.6577 (t) REVERT: A 261 ASP cc_start: 0.7874 (t0) cc_final: 0.7586 (t0) REVERT: A 276 GLU cc_start: 0.9229 (mp0) cc_final: 0.8954 (mp0) REVERT: A 337 ASP cc_start: 0.8219 (m-30) cc_final: 0.7875 (m-30) REVERT: B 266 HIS cc_start: 0.7811 (t-170) cc_final: 0.7355 (t-170) REVERT: B 339 TRP cc_start: 0.8625 (m100) cc_final: 0.7954 (m-10) REVERT: B 340 ASN cc_start: 0.7249 (t0) cc_final: 0.6573 (t0) REVERT: C 40 TYR cc_start: 0.8674 (t80) cc_final: 0.8463 (t80) REVERT: R 86 ASN cc_start: 0.8522 (m-40) cc_final: 0.8255 (m-40) REVERT: R 262 ARG cc_start: 0.7373 (mtp85) cc_final: 0.7040 (mtm180) REVERT: R 301 LYS cc_start: 0.8392 (tttt) cc_final: 0.8121 (ttmm) REVERT: P 34 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7421 (tm-30) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1073 time to fit residues: 34.0678 Evaluate side-chains 166 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 62 HIS B 119 ASN B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN R 100 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 260 HIS R 261 GLN R 288 GLN R 311 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.120399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095266 restraints weight = 16946.342| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.95 r_work: 0.3359 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7392 Z= 0.176 Angle : 0.650 8.548 10052 Z= 0.331 Chirality : 0.045 0.278 1183 Planarity : 0.005 0.050 1262 Dihedral : 5.207 59.933 1022 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.30 % Allowed : 14.66 % Favored : 82.03 % 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: -2.33 (0.26), residues: 931 helix: 0.27 (0.26), residues: 398 sheet: -2.85 (0.36), residues: 162 loop : -2.95 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 251 TYR 0.029 0.002 TYR P 21 PHE 0.021 0.002 PHE R 340 TRP 0.029 0.003 TRP R 116 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 7391) covalent geometry : angle 0.64985 (10050) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.61243 ( 2) hydrogen bonds : bond 0.03649 ( 337) hydrogen bonds : angle 4.81192 ( 963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9256 (tm-30) cc_final: 0.9036 (tm-30) REVERT: A 33 GLU cc_start: 0.9070 (pp20) cc_final: 0.8033 (pp20) REVERT: A 191 PHE cc_start: 0.8452 (t80) cc_final: 0.7947 (t80) REVERT: A 195 HIS cc_start: 0.8531 (m-70) cc_final: 0.7703 (m-70) REVERT: A 231 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8699 (m-30) REVERT: A 261 ASP cc_start: 0.8448 (t0) cc_final: 0.8103 (t0) REVERT: A 276 GLU cc_start: 0.9405 (mp0) cc_final: 0.9081 (mp0) REVERT: A 337 ASP cc_start: 0.8647 (m-30) cc_final: 0.8111 (m-30) REVERT: A 341 ASP cc_start: 0.8576 (t70) cc_final: 0.8361 (t0) REVERT: B 45 MET cc_start: 0.8280 (mmt) cc_final: 0.8004 (mmt) REVERT: B 72 SER cc_start: 0.8349 (m) cc_final: 0.8043 (p) REVERT: B 209 LYS cc_start: 0.7513 (mttt) cc_final: 0.7054 (mttm) REVERT: B 211 TRP cc_start: 0.7212 (m100) cc_final: 0.6130 (m100) REVERT: B 215 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8218 (pt0) REVERT: B 266 HIS cc_start: 0.8495 (t-170) cc_final: 0.8007 (t70) REVERT: B 339 TRP cc_start: 0.8779 (m100) cc_final: 0.8161 (m100) REVERT: C 40 TYR cc_start: 0.8773 (t80) cc_final: 0.8533 (t80) REVERT: R 116 TRP cc_start: 0.8076 (t-100) cc_final: 0.7721 (t60) REVERT: R 262 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7365 (mtm180) REVERT: R 301 LYS cc_start: 0.8665 (tttt) cc_final: 0.8298 (ttmm) REVERT: P 15 GLU cc_start: 0.8730 (pm20) cc_final: 0.8378 (pm20) outliers start: 25 outliers final: 14 residues processed: 199 average time/residue: 0.0967 time to fit residues: 25.4183 Evaluate side-chains 176 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 259 GLN R 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.117868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092389 restraints weight = 16510.581| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.88 r_work: 0.3335 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7392 Z= 0.147 Angle : 0.612 8.178 10052 Z= 0.307 Chirality : 0.043 0.191 1183 Planarity : 0.004 0.049 1262 Dihedral : 5.199 58.725 1022 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.23 % Allowed : 15.98 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.87 (0.27), residues: 931 helix: 0.64 (0.27), residues: 394 sheet: -2.45 (0.39), residues: 150 loop : -2.77 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 25 TYR 0.015 0.001 TYR P 20 PHE 0.015 0.001 PHE B 335 TRP 0.027 0.002 TRP B 297 HIS 0.004 0.001 HIS R 73 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7391) covalent geometry : angle 0.61175 (10050) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.35482 ( 2) hydrogen bonds : bond 0.03414 ( 337) hydrogen bonds : angle 4.68587 ( 963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9256 (tm-30) cc_final: 0.9039 (tm-30) REVERT: A 33 GLU cc_start: 0.9074 (pp20) cc_final: 0.8570 (pp20) REVERT: A 191 PHE cc_start: 0.8472 (t80) cc_final: 0.8087 (t80) REVERT: A 195 HIS cc_start: 0.8565 (m-70) cc_final: 0.8073 (m-70) REVERT: A 231 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8737 (m-30) REVERT: A 243 MET cc_start: 0.8886 (ttm) cc_final: 0.8619 (ttm) REVERT: A 261 ASP cc_start: 0.8451 (t0) cc_final: 0.8034 (t0) REVERT: A 276 GLU cc_start: 0.9403 (mp0) cc_final: 0.9059 (mp0) REVERT: A 315 ASP cc_start: 0.8080 (p0) cc_final: 0.7812 (p0) REVERT: A 337 ASP cc_start: 0.8654 (m-30) cc_final: 0.8041 (m-30) REVERT: B 45 MET cc_start: 0.8306 (mmt) cc_final: 0.7894 (mmt) REVERT: B 59 TYR cc_start: 0.8546 (m-80) cc_final: 0.8345 (m-80) REVERT: B 209 LYS cc_start: 0.7538 (mttt) cc_final: 0.6940 (mttm) REVERT: B 211 TRP cc_start: 0.7167 (m100) cc_final: 0.6147 (m100) REVERT: B 215 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8110 (tm-30) REVERT: B 266 HIS cc_start: 0.8442 (t-170) cc_final: 0.7972 (t70) REVERT: B 292 PHE cc_start: 0.8167 (m-10) cc_final: 0.7889 (m-80) REVERT: B 339 TRP cc_start: 0.8817 (m100) cc_final: 0.8187 (m100) REVERT: C 40 TYR cc_start: 0.8769 (t80) cc_final: 0.8506 (t80) REVERT: R 146 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8709 (mm) REVERT: R 215 TYR cc_start: 0.7208 (m-80) cc_final: 0.6486 (t80) REVERT: R 262 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7352 (mtm-85) REVERT: R 301 LYS cc_start: 0.8664 (tttt) cc_final: 0.8300 (ttmm) REVERT: P 21 TYR cc_start: 0.7905 (m-80) cc_final: 0.7667 (m-80) outliers start: 32 outliers final: 15 residues processed: 193 average time/residue: 0.0902 time to fit residues: 23.3485 Evaluate side-chains 176 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.121085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095716 restraints weight = 16811.807| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.00 r_work: 0.3349 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7392 Z= 0.121 Angle : 0.614 9.415 10052 Z= 0.303 Chirality : 0.043 0.178 1183 Planarity : 0.004 0.048 1262 Dihedral : 5.125 56.717 1022 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.96 % Allowed : 17.83 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.70 (0.27), residues: 931 helix: 0.76 (0.27), residues: 394 sheet: -2.48 (0.39), residues: 154 loop : -2.59 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.015 0.001 TYR R 303 PHE 0.014 0.001 PHE R 340 TRP 0.026 0.001 TRP B 297 HIS 0.003 0.001 HIS R 73 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7391) covalent geometry : angle 0.61363 (10050) SS BOND : bond 0.00300 ( 1) SS BOND : angle 1.36368 ( 2) hydrogen bonds : bond 0.03211 ( 337) hydrogen bonds : angle 4.54855 ( 963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9238 (tm-30) cc_final: 0.9028 (tm-30) REVERT: A 33 GLU cc_start: 0.9081 (pp20) cc_final: 0.8583 (pp20) REVERT: A 35 LYS cc_start: 0.9041 (mppt) cc_final: 0.8631 (mptt) REVERT: A 190 THR cc_start: 0.8098 (m) cc_final: 0.7612 (m) REVERT: A 191 PHE cc_start: 0.8492 (t80) cc_final: 0.8075 (t80) REVERT: A 195 HIS cc_start: 0.8592 (m-70) cc_final: 0.7727 (m-70) REVERT: A 231 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8697 (m-30) REVERT: A 243 MET cc_start: 0.8819 (ttm) cc_final: 0.8571 (ttm) REVERT: A 261 ASP cc_start: 0.8474 (t0) cc_final: 0.8053 (t0) REVERT: A 276 GLU cc_start: 0.9410 (mp0) cc_final: 0.9046 (mp0) REVERT: A 315 ASP cc_start: 0.8107 (p0) cc_final: 0.7823 (p0) REVERT: A 337 ASP cc_start: 0.8762 (m-30) cc_final: 0.8052 (m-30) REVERT: B 45 MET cc_start: 0.8328 (mmt) cc_final: 0.7924 (mmp) REVERT: B 59 TYR cc_start: 0.8464 (m-80) cc_final: 0.8186 (m-80) REVERT: B 78 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7693 (mmmt) REVERT: B 209 LYS cc_start: 0.7505 (mttt) cc_final: 0.6821 (mttt) REVERT: B 211 TRP cc_start: 0.7119 (m100) cc_final: 0.6037 (m100) REVERT: B 215 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8117 (tm-30) REVERT: B 259 GLN cc_start: 0.6757 (OUTLIER) cc_final: 0.6491 (pt0) REVERT: B 266 HIS cc_start: 0.8383 (t-170) cc_final: 0.7966 (t70) REVERT: B 292 PHE cc_start: 0.8229 (m-10) cc_final: 0.7998 (m-10) REVERT: B 339 TRP cc_start: 0.8854 (m100) cc_final: 0.8311 (m100) REVERT: C 40 TYR cc_start: 0.8755 (t80) cc_final: 0.8496 (t80) REVERT: R 108 LEU cc_start: 0.9281 (tp) cc_final: 0.9050 (mp) REVERT: R 116 TRP cc_start: 0.8045 (t-100) cc_final: 0.7841 (t60) REVERT: R 146 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8667 (mm) REVERT: R 262 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7315 (mtm-85) REVERT: R 301 LYS cc_start: 0.8672 (tttt) cc_final: 0.8254 (ttmm) REVERT: P 15 GLU cc_start: 0.8600 (pm20) cc_final: 0.8313 (pm20) outliers start: 30 outliers final: 17 residues processed: 192 average time/residue: 0.0913 time to fit residues: 23.5621 Evaluate side-chains 177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 0.0370 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 75 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 100 ASN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.119805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094188 restraints weight = 16472.851| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.93 r_work: 0.3370 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7392 Z= 0.112 Angle : 0.603 9.106 10052 Z= 0.297 Chirality : 0.043 0.288 1183 Planarity : 0.004 0.045 1262 Dihedral : 5.043 55.009 1022 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.57 % Allowed : 18.89 % Favored : 77.54 % 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: -1.53 (0.27), residues: 931 helix: 0.82 (0.27), residues: 398 sheet: -2.34 (0.41), residues: 149 loop : -2.46 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.025 0.001 TYR P 21 PHE 0.013 0.001 PHE R 287 TRP 0.017 0.001 TRP B 297 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7391) covalent geometry : angle 0.60265 (10050) SS BOND : bond 0.00149 ( 1) SS BOND : angle 1.14947 ( 2) hydrogen bonds : bond 0.03144 ( 337) hydrogen bonds : angle 4.43246 ( 963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.9081 (pp20) cc_final: 0.8230 (pp20) REVERT: A 35 LYS cc_start: 0.9049 (mppt) cc_final: 0.8709 (mptt) REVERT: A 191 PHE cc_start: 0.8458 (t80) cc_final: 0.8095 (t80) REVERT: A 243 MET cc_start: 0.8761 (ttm) cc_final: 0.8523 (ttm) REVERT: A 261 ASP cc_start: 0.8486 (t0) cc_final: 0.8129 (t0) REVERT: A 276 GLU cc_start: 0.9406 (mp0) cc_final: 0.9029 (mp0) REVERT: A 315 ASP cc_start: 0.8048 (p0) cc_final: 0.7742 (p0) REVERT: A 337 ASP cc_start: 0.8761 (m-30) cc_final: 0.8029 (m-30) REVERT: B 45 MET cc_start: 0.8324 (mmt) cc_final: 0.7932 (mmp) REVERT: B 78 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7731 (mmmt) REVERT: B 215 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8111 (tm-30) REVERT: B 266 HIS cc_start: 0.8320 (t-170) cc_final: 0.7925 (t70) REVERT: B 292 PHE cc_start: 0.8204 (m-10) cc_final: 0.7978 (m-10) REVERT: B 339 TRP cc_start: 0.8813 (m100) cc_final: 0.8421 (m100) REVERT: C 40 TYR cc_start: 0.8743 (t80) cc_final: 0.8480 (t80) REVERT: R 116 TRP cc_start: 0.7998 (t-100) cc_final: 0.7779 (t60) REVERT: R 146 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8675 (mm) REVERT: R 262 ARG cc_start: 0.7836 (mtp85) cc_final: 0.7305 (mtm180) REVERT: R 301 LYS cc_start: 0.8653 (tttt) cc_final: 0.8319 (ttmm) outliers start: 27 outliers final: 20 residues processed: 192 average time/residue: 0.0858 time to fit residues: 22.1031 Evaluate side-chains 180 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 259 TYR Chi-restraints excluded: chain R residue 263 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 36 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 70 optimal weight: 0.0050 chunk 2 optimal weight: 6.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 GLN R 249 HIS ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.116486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090918 restraints weight = 16630.510| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.89 r_work: 0.3301 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7392 Z= 0.160 Angle : 0.646 12.506 10052 Z= 0.323 Chirality : 0.045 0.388 1183 Planarity : 0.004 0.046 1262 Dihedral : 5.119 53.627 1022 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.83 % Allowed : 21.40 % Favored : 74.77 % 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: -1.51 (0.27), residues: 931 helix: 0.81 (0.27), residues: 398 sheet: -2.33 (0.39), residues: 159 loop : -2.40 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 21 TYR 0.017 0.001 TYR R 110 PHE 0.011 0.001 PHE R 319 TRP 0.015 0.001 TRP B 297 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7391) covalent geometry : angle 0.64520 (10050) SS BOND : bond 0.00071 ( 1) SS BOND : angle 2.07023 ( 2) hydrogen bonds : bond 0.03242 ( 337) hydrogen bonds : angle 4.51121 ( 963) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8470 (pp20) REVERT: A 33 GLU cc_start: 0.9083 (pp20) cc_final: 0.8601 (pp20) REVERT: A 35 LYS cc_start: 0.9097 (mppt) cc_final: 0.8683 (mptt) REVERT: A 36 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8110 (mp) REVERT: A 191 PHE cc_start: 0.8419 (t80) cc_final: 0.7993 (t80) REVERT: A 195 HIS cc_start: 0.8633 (m-70) cc_final: 0.7871 (m-70) REVERT: A 205 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.8144 (mtm-85) REVERT: A 243 MET cc_start: 0.8801 (ttm) cc_final: 0.8561 (ttm) REVERT: A 261 ASP cc_start: 0.8473 (t0) cc_final: 0.8060 (t0) REVERT: A 276 GLU cc_start: 0.9415 (mp0) cc_final: 0.9018 (mp0) REVERT: A 315 ASP cc_start: 0.8097 (p0) cc_final: 0.7751 (p0) REVERT: A 337 ASP cc_start: 0.8834 (m-30) cc_final: 0.8120 (m-30) REVERT: B 45 MET cc_start: 0.8460 (mmt) cc_final: 0.8044 (mmp) REVERT: B 59 TYR cc_start: 0.8511 (m-80) cc_final: 0.8185 (m-80) REVERT: B 124 TYR cc_start: 0.8600 (m-80) cc_final: 0.8157 (m-80) REVERT: B 215 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8370 (tt0) REVERT: B 266 HIS cc_start: 0.8319 (t-170) cc_final: 0.7745 (t-170) REVERT: B 339 TRP cc_start: 0.8855 (m100) cc_final: 0.8352 (m100) REVERT: C 36 ASP cc_start: 0.9009 (m-30) cc_final: 0.8286 (t0) REVERT: C 40 TYR cc_start: 0.8746 (t80) cc_final: 0.8484 (t80) REVERT: C 46 LYS cc_start: 0.7785 (ptpp) cc_final: 0.7403 (tptt) REVERT: C 47 GLU cc_start: 0.8367 (pm20) cc_final: 0.8021 (pm20) REVERT: R 108 LEU cc_start: 0.9224 (tp) cc_final: 0.8996 (mp) REVERT: R 135 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8595 (mm-40) REVERT: R 146 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8790 (mm) REVERT: R 215 TYR cc_start: 0.7287 (m-80) cc_final: 0.6546 (t80) REVERT: R 262 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7477 (mtm180) REVERT: R 301 LYS cc_start: 0.8636 (tttt) cc_final: 0.8325 (ttmm) REVERT: P 21 TYR cc_start: 0.8120 (m-80) cc_final: 0.7738 (m-80) outliers start: 29 outliers final: 20 residues processed: 181 average time/residue: 0.0862 time to fit residues: 20.8021 Evaluate side-chains 174 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 259 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 5 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 GLN ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN ** P 34 GLN ** 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 = 0.3873 r_free = 0.3873 target = 0.119866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.094385 restraints weight = 16649.906| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.95 r_work: 0.3341 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7392 Z= 0.121 Angle : 0.648 14.055 10052 Z= 0.316 Chirality : 0.044 0.430 1183 Planarity : 0.004 0.047 1262 Dihedral : 4.987 50.740 1022 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.83 % Allowed : 21.66 % Favored : 74.50 % 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: -1.35 (0.27), residues: 931 helix: 0.91 (0.27), residues: 397 sheet: -2.28 (0.40), residues: 154 loop : -2.25 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.015 0.001 TYR P 20 PHE 0.016 0.001 PHE B 292 TRP 0.011 0.001 TRP B 297 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7391) covalent geometry : angle 0.64754 (10050) SS BOND : bond 0.00180 ( 1) SS BOND : angle 1.69635 ( 2) hydrogen bonds : bond 0.03154 ( 337) hydrogen bonds : angle 4.45833 ( 963) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8800 (pp20) REVERT: A 33 GLU cc_start: 0.9074 (pp20) cc_final: 0.8256 (pp20) REVERT: A 35 LYS cc_start: 0.9048 (mppt) cc_final: 0.8700 (mptt) REVERT: A 191 PHE cc_start: 0.8432 (t80) cc_final: 0.7978 (t80) REVERT: A 195 HIS cc_start: 0.8585 (m-70) cc_final: 0.7613 (m-70) REVERT: A 205 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8176 (mtm-85) REVERT: A 243 MET cc_start: 0.8771 (ttm) cc_final: 0.8562 (ttm) REVERT: A 261 ASP cc_start: 0.8491 (t0) cc_final: 0.8138 (t0) REVERT: A 276 GLU cc_start: 0.9405 (mp0) cc_final: 0.9012 (mp0) REVERT: A 315 ASP cc_start: 0.8116 (p0) cc_final: 0.7780 (p0) REVERT: A 337 ASP cc_start: 0.8780 (m-30) cc_final: 0.8057 (m-30) REVERT: B 45 MET cc_start: 0.8416 (mmt) cc_final: 0.8014 (mmp) REVERT: B 59 TYR cc_start: 0.8421 (m-80) cc_final: 0.8134 (m-80) REVERT: B 124 TYR cc_start: 0.8513 (m-80) cc_final: 0.8123 (m-80) REVERT: B 215 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8398 (tt0) REVERT: B 266 HIS cc_start: 0.8361 (t-170) cc_final: 0.7786 (t-170) REVERT: B 292 PHE cc_start: 0.8255 (m-10) cc_final: 0.7961 (m-80) REVERT: B 325 MET cc_start: 0.6849 (tpp) cc_final: 0.6507 (tpp) REVERT: B 339 TRP cc_start: 0.8825 (m100) cc_final: 0.8465 (m100) REVERT: C 36 ASP cc_start: 0.8987 (m-30) cc_final: 0.8260 (t0) REVERT: C 40 TYR cc_start: 0.8749 (t80) cc_final: 0.8508 (t80) REVERT: C 46 LYS cc_start: 0.7827 (ptpp) cc_final: 0.7415 (tptt) REVERT: R 108 LEU cc_start: 0.9218 (tp) cc_final: 0.8953 (mp) REVERT: R 146 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8736 (mm) REVERT: R 262 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7362 (mtm-85) REVERT: R 301 LYS cc_start: 0.8643 (tttt) cc_final: 0.8355 (ttmm) outliers start: 29 outliers final: 21 residues processed: 186 average time/residue: 0.0853 time to fit residues: 21.0906 Evaluate side-chains 179 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 298 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 78 optimal weight: 0.0470 chunk 19 optimal weight: 0.0470 chunk 72 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 84 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN ** P 34 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.121408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095862 restraints weight = 16605.779| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.99 r_work: 0.3395 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7392 Z= 0.114 Angle : 0.657 14.772 10052 Z= 0.320 Chirality : 0.044 0.440 1183 Planarity : 0.004 0.045 1262 Dihedral : 4.507 40.124 1022 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.64 % Allowed : 23.51 % Favored : 73.84 % 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: -1.22 (0.27), residues: 931 helix: 0.95 (0.26), residues: 397 sheet: -2.09 (0.41), residues: 154 loop : -2.16 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 21 TYR 0.024 0.001 TYR R 110 PHE 0.010 0.001 PHE R 340 TRP 0.014 0.001 TRP R 116 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7391) covalent geometry : angle 0.65679 (10050) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.09040 ( 2) hydrogen bonds : bond 0.03057 ( 337) hydrogen bonds : angle 4.38422 ( 963) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8797 (pp20) REVERT: A 33 GLU cc_start: 0.8997 (pp20) cc_final: 0.8250 (pp20) REVERT: A 35 LYS cc_start: 0.9044 (mppt) cc_final: 0.8687 (mptt) REVERT: A 36 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7959 (mp) REVERT: A 191 PHE cc_start: 0.8417 (t80) cc_final: 0.7891 (t80) REVERT: A 195 HIS cc_start: 0.8592 (m-70) cc_final: 0.7648 (m-70) REVERT: A 205 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: A 261 ASP cc_start: 0.8500 (t0) cc_final: 0.8187 (t0) REVERT: A 275 GLU cc_start: 0.8990 (tp30) cc_final: 0.8675 (mm-30) REVERT: A 276 GLU cc_start: 0.9394 (mp0) cc_final: 0.9013 (mp0) REVERT: A 315 ASP cc_start: 0.8105 (p0) cc_final: 0.7756 (p0) REVERT: A 337 ASP cc_start: 0.8759 (m-30) cc_final: 0.8006 (m-30) REVERT: B 45 MET cc_start: 0.8363 (mmt) cc_final: 0.8021 (mmt) REVERT: B 59 TYR cc_start: 0.8308 (m-80) cc_final: 0.8077 (m-80) REVERT: B 78 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7676 (mmmt) REVERT: B 124 TYR cc_start: 0.8420 (m-80) cc_final: 0.8095 (m-80) REVERT: B 215 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8433 (tt0) REVERT: B 266 HIS cc_start: 0.8355 (t-170) cc_final: 0.7877 (t70) REVERT: B 292 PHE cc_start: 0.8113 (m-10) cc_final: 0.7759 (m-80) REVERT: B 325 MET cc_start: 0.6779 (tpp) cc_final: 0.6447 (tpp) REVERT: B 339 TRP cc_start: 0.8826 (m100) cc_final: 0.8501 (m100) REVERT: C 36 ASP cc_start: 0.8999 (m-30) cc_final: 0.8290 (t0) REVERT: C 40 TYR cc_start: 0.8731 (t80) cc_final: 0.8505 (t80) REVERT: C 46 LYS cc_start: 0.7876 (ptpp) cc_final: 0.7424 (tptt) REVERT: R 146 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8675 (mm) REVERT: R 262 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7358 (mtm180) REVERT: R 301 LYS cc_start: 0.8590 (tttt) cc_final: 0.8293 (ttmm) REVERT: R 307 PHE cc_start: 0.8326 (t80) cc_final: 0.7840 (t80) REVERT: P 21 TYR cc_start: 0.8172 (m-80) cc_final: 0.7817 (m-80) outliers start: 20 outliers final: 17 residues processed: 184 average time/residue: 0.0899 time to fit residues: 22.0875 Evaluate side-chains 180 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 298 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 0.5980 chunk 70 optimal weight: 0.0670 chunk 27 optimal weight: 0.0270 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 0.0170 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 0.3414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN ** P 34 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.124181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099141 restraints weight = 16448.684| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 4.01 r_work: 0.3405 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7392 Z= 0.114 Angle : 0.671 15.296 10052 Z= 0.321 Chirality : 0.044 0.447 1183 Planarity : 0.003 0.045 1262 Dihedral : 4.070 24.833 1022 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.25 % Allowed : 24.31 % Favored : 73.45 % 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: -1.09 (0.28), residues: 931 helix: 1.02 (0.27), residues: 397 sheet: -1.90 (0.43), residues: 138 loop : -2.13 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 21 TYR 0.012 0.001 TYR R 228 PHE 0.016 0.001 PHE B 222 TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 7391) covalent geometry : angle 0.67066 (10050) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.63000 ( 2) hydrogen bonds : bond 0.03064 ( 337) hydrogen bonds : angle 4.33155 ( 963) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8860 (pp20) REVERT: A 21 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8466 (ttp-110) REVERT: A 33 GLU cc_start: 0.8978 (pp20) cc_final: 0.8213 (pp20) REVERT: A 35 LYS cc_start: 0.9022 (mppt) cc_final: 0.8657 (mptt) REVERT: A 191 PHE cc_start: 0.8428 (t80) cc_final: 0.7942 (t80) REVERT: A 195 HIS cc_start: 0.8615 (m-70) cc_final: 0.7672 (m-70) REVERT: A 205 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.8183 (mtm-85) REVERT: A 261 ASP cc_start: 0.8530 (t0) cc_final: 0.8206 (t0) REVERT: A 275 GLU cc_start: 0.8983 (tp30) cc_final: 0.8703 (mm-30) REVERT: A 276 GLU cc_start: 0.9391 (mp0) cc_final: 0.9014 (mp0) REVERT: A 315 ASP cc_start: 0.8096 (p0) cc_final: 0.7724 (p0) REVERT: A 337 ASP cc_start: 0.8699 (m-30) cc_final: 0.7968 (m-30) REVERT: B 59 TYR cc_start: 0.8264 (m-80) cc_final: 0.8045 (m-80) REVERT: B 78 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7623 (mmmt) REVERT: B 124 TYR cc_start: 0.8401 (m-80) cc_final: 0.8064 (m-80) REVERT: B 215 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8473 (tt0) REVERT: B 266 HIS cc_start: 0.8345 (t-170) cc_final: 0.7880 (t70) REVERT: B 292 PHE cc_start: 0.8070 (m-10) cc_final: 0.7728 (m-80) REVERT: B 325 MET cc_start: 0.6717 (tpp) cc_final: 0.6397 (tpp) REVERT: B 339 TRP cc_start: 0.8814 (m100) cc_final: 0.8600 (m100) REVERT: C 36 ASP cc_start: 0.8989 (m-30) cc_final: 0.8300 (t0) REVERT: C 40 TYR cc_start: 0.8716 (t80) cc_final: 0.8510 (t80) REVERT: C 46 LYS cc_start: 0.7883 (ptpp) cc_final: 0.7446 (tptt) REVERT: R 146 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8632 (mm) REVERT: R 204 THR cc_start: 0.8190 (p) cc_final: 0.7754 (p) REVERT: R 205 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8285 (mm-30) REVERT: R 262 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7320 (mtm180) REVERT: R 301 LYS cc_start: 0.8564 (tttt) cc_final: 0.8288 (ttmm) REVERT: P 21 TYR cc_start: 0.8175 (m-80) cc_final: 0.7793 (m-80) outliers start: 17 outliers final: 15 residues processed: 178 average time/residue: 0.0856 time to fit residues: 20.4247 Evaluate side-chains 177 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 GLN ** P 34 GLN ** 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 = 0.3846 r_free = 0.3846 target = 0.117862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092295 restraints weight = 16559.180| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.89 r_work: 0.3302 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7392 Z= 0.174 Angle : 0.729 16.929 10052 Z= 0.351 Chirality : 0.047 0.449 1183 Planarity : 0.004 0.045 1262 Dihedral : 4.138 20.148 1022 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.17 % Allowed : 24.44 % Favored : 72.39 % 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: -1.11 (0.28), residues: 931 helix: 1.05 (0.27), residues: 390 sheet: -2.12 (0.39), residues: 161 loop : -1.99 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 21 TYR 0.037 0.002 TYR R 110 PHE 0.023 0.002 PHE B 222 TRP 0.019 0.002 TRP R 116 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7391) covalent geometry : angle 0.72850 (10050) SS BOND : bond 0.00181 ( 1) SS BOND : angle 1.41763 ( 2) hydrogen bonds : bond 0.03327 ( 337) hydrogen bonds : angle 4.44188 ( 963) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8855 (pp20) REVERT: A 18 MET cc_start: 0.8920 (ttm) cc_final: 0.8550 (tpp) REVERT: A 33 GLU cc_start: 0.8974 (pp20) cc_final: 0.8218 (pp20) REVERT: A 35 LYS cc_start: 0.9086 (mppt) cc_final: 0.8725 (mptt) REVERT: A 191 PHE cc_start: 0.8401 (t80) cc_final: 0.7957 (t80) REVERT: A 195 HIS cc_start: 0.8620 (m-70) cc_final: 0.7645 (m-70) REVERT: A 205 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8141 (mtm-85) REVERT: A 261 ASP cc_start: 0.8550 (t0) cc_final: 0.8202 (t0) REVERT: A 276 GLU cc_start: 0.9416 (mp0) cc_final: 0.9021 (mp0) REVERT: A 315 ASP cc_start: 0.8148 (p0) cc_final: 0.7771 (p0) REVERT: A 337 ASP cc_start: 0.8822 (m-30) cc_final: 0.8111 (m-30) REVERT: B 23 LYS cc_start: 0.8553 (tptt) cc_final: 0.8204 (tptp) REVERT: B 59 TYR cc_start: 0.8603 (m-80) cc_final: 0.8354 (m-80) REVERT: B 78 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7638 (mmmt) REVERT: B 124 TYR cc_start: 0.8576 (m-80) cc_final: 0.8102 (m-80) REVERT: B 215 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8457 (tt0) REVERT: B 266 HIS cc_start: 0.8443 (t-170) cc_final: 0.7816 (t-170) REVERT: B 292 PHE cc_start: 0.8256 (m-10) cc_final: 0.8004 (m-80) REVERT: B 325 MET cc_start: 0.6924 (tpp) cc_final: 0.6690 (tpp) REVERT: B 339 TRP cc_start: 0.8827 (m100) cc_final: 0.8484 (m100) REVERT: C 36 ASP cc_start: 0.8997 (m-30) cc_final: 0.8304 (t0) REVERT: C 40 TYR cc_start: 0.8749 (t80) cc_final: 0.8495 (t80) REVERT: R 108 LEU cc_start: 0.9215 (tp) cc_final: 0.8936 (mp) REVERT: R 116 TRP cc_start: 0.7647 (t-100) cc_final: 0.7411 (t-100) REVERT: R 215 TYR cc_start: 0.7291 (m-80) cc_final: 0.6591 (t80) REVERT: R 262 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7483 (mtm180) REVERT: P 21 TYR cc_start: 0.8185 (m-80) cc_final: 0.7767 (m-80) REVERT: P 34 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8174 (pp30) outliers start: 24 outliers final: 17 residues processed: 178 average time/residue: 0.0859 time to fit residues: 20.4188 Evaluate side-chains 167 residues out of total 816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.119763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094002 restraints weight = 16520.437| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.95 r_work: 0.3332 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7392 Z= 0.138 Angle : 0.727 15.446 10052 Z= 0.345 Chirality : 0.046 0.423 1183 Planarity : 0.004 0.045 1262 Dihedral : 4.085 20.634 1022 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.77 % Allowed : 25.10 % Favored : 72.13 % 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: -1.09 (0.28), residues: 931 helix: 1.03 (0.27), residues: 390 sheet: -2.04 (0.42), residues: 139 loop : -2.01 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.012 0.001 TYR P 20 PHE 0.020 0.001 PHE R 307 TRP 0.016 0.001 TRP R 116 HIS 0.008 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 7391) covalent geometry : angle 0.72725 (10050) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.95952 ( 2) hydrogen bonds : bond 0.03209 ( 337) hydrogen bonds : angle 4.48609 ( 963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.16 seconds wall clock time: 34 minutes 2.71 seconds (2042.71 seconds total)