Starting phenix.real_space_refine on Wed Sep 17 13:34:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blc_44653/09_2025/9blc_44653.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blc_44653/09_2025/9blc_44653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blc_44653/09_2025/9blc_44653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blc_44653/09_2025/9blc_44653.map" model { file = "/net/cci-nas-00/data/ceres_data/9blc_44653/09_2025/9blc_44653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blc_44653/09_2025/9blc_44653.cif" } resolution = 3.3 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= -0.002 sd= 0.037 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 64 5.16 5 C 5721 2.51 5 N 1582 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 9015 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 234 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 16, 'TRANS': 353} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 6, 'ARG:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 4, 'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Time building chain proxies: 2.40, per 1000 atoms: 0.27 Number of scatterers: 9015 At special positions: 0 Unit cell: (81.7, 101.48, 149.64, 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 64 16.00 O 1648 8.00 N 1582 7.00 C 5721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.09 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 316.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 41.8% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'P' and resid 4 through 7 Processing helix chain 'P' and resid 8 through 21 removed outlier: 3.621A pdb=" N ASN P 21 " --> pdb=" O ARG P 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 62 removed outlier: 3.611A pdb=" N MET R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 3.640A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA R 136 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.806A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.660A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 4.089A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.700A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 221 " --> pdb=" O VAL R 217 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 285 Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.670A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.963A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 removed outlier: 4.062A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.594A pdb=" N HIS R 377 " --> pdb=" O ASP R 373 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 393 Processing helix chain 'R' and resid 395 through 413 Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.679A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.645A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.525A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.520A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.588A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.762A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 53 through 56 Processing sheet with id=AA1, first strand: chain 'R' and resid 91 through 94 removed outlier: 3.532A pdb=" N LYS R 110 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.808A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.366A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.661A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.032A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.630A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.639A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.982A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.656A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.103A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.707A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.443A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1254 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: 1.46 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2929 1.34 - 1.46: 2275 1.46 - 1.59: 3921 1.59 - 1.72: 0 1.72 - 1.85: 90 Bond restraints: 9215 Sorted by residual: bond pdb=" N PRO R 363 " pdb=" CD PRO R 363 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.481 -0.028 9.20e-03 1.18e+04 9.10e+00 bond pdb=" N TRP R 361 " pdb=" CA TRP R 361 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.55e+00 bond pdb=" N ASN R 365 " pdb=" CA ASN R 365 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.22e-02 6.72e+03 7.40e+00 bond pdb=" N VAL R 358 " pdb=" CA VAL R 358 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.21e-02 6.83e+03 7.26e+00 ... (remaining 9210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 12273 1.73 - 3.45: 188 3.45 - 5.18: 27 5.18 - 6.91: 5 6.91 - 8.63: 1 Bond angle restraints: 12494 Sorted by residual: angle pdb=" N GLY P 33 " pdb=" CA GLY P 33 " pdb=" C GLY P 33 " ideal model delta sigma weight residual 112.50 117.28 -4.78 1.16e+00 7.43e-01 1.70e+01 angle pdb=" N PRO R 360 " pdb=" CA PRO R 360 " pdb=" C PRO R 360 " ideal model delta sigma weight residual 113.40 118.51 -5.11 1.34e+00 5.57e-01 1.46e+01 angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 121.00 117.06 3.94 1.08e+00 8.57e-01 1.33e+01 angle pdb=" N LEU R 368 " pdb=" CA LEU R 368 " pdb=" C LEU R 368 " ideal model delta sigma weight residual 111.28 107.50 3.78 1.09e+00 8.42e-01 1.20e+01 angle pdb=" C ASP R 373 " pdb=" CA ASP R 373 " pdb=" CB ASP R 373 " ideal model delta sigma weight residual 110.85 116.36 -5.51 1.70e+00 3.46e-01 1.05e+01 ... (remaining 12489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4769 17.83 - 35.67: 532 35.67 - 53.50: 133 53.50 - 71.33: 22 71.33 - 89.16: 12 Dihedral angle restraints: 5468 sinusoidal: 2114 harmonic: 3354 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 178.80 -85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 154.22 -61.22 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual -86.00 -133.04 47.04 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 5465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1232 0.064 - 0.127: 147 0.127 - 0.191: 6 0.191 - 0.254: 4 0.254 - 0.318: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA ASP R 373 " pdb=" N ASP R 373 " pdb=" C ASP R 373 " pdb=" CB ASP R 373 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA PHE R 359 " pdb=" N PHE R 359 " pdb=" C PHE R 359 " pdb=" CB PHE R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA PRO R 360 " pdb=" N PRO R 360 " pdb=" C PRO R 360 " pdb=" CB PRO R 360 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1388 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 362 " -0.069 5.00e-02 4.00e+02 1.07e-01 1.82e+01 pdb=" N PRO R 363 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO R 363 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO R 363 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO G 60 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 194 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.025 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 227 2.70 - 3.25: 8695 3.25 - 3.80: 14049 3.80 - 4.35: 18129 4.35 - 4.90: 31075 Nonbonded interactions: 72175 Sorted by model distance: nonbonded pdb=" OE1 GLN R 408 " pdb=" O ALA B 309 " model vdw 2.146 3.040 nonbonded pdb=" O ASP A 215 " pdb=" OD1 ASP A 215 " model vdw 2.217 3.040 nonbonded pdb=" OD1 ASP R 103 " pdb=" N SER R 105 " model vdw 2.238 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.258 3.040 ... (remaining 72170 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=0.00 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 9223 Z= 0.200 Angle : 0.531 8.634 12508 Z= 0.314 Chirality : 0.043 0.318 1391 Planarity : 0.004 0.107 1599 Dihedral : 16.165 89.163 3275 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.21 % Favored : 97.70 % Rotamer: Outliers : 0.84 % Allowed : 22.44 % Favored : 76.71 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.25), residues: 1132 helix: 1.51 (0.25), residues: 436 sheet: -0.52 (0.34), residues: 233 loop : -0.76 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.010 0.001 TYR N 95 PHE 0.018 0.001 PHE R 285 TRP 0.009 0.001 TRP A 234 HIS 0.006 0.001 HIS R 184 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9215) covalent geometry : angle 0.52468 (12494) SS BOND : bond 0.02062 ( 7) SS BOND : angle 2.53049 ( 14) hydrogen bonds : bond 0.22604 ( 437) hydrogen bonds : angle 7.22377 ( 1254) Misc. bond : bond 0.09346 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 9 ILE cc_start: 0.6924 (tt) cc_final: 0.5777 (tp) REVERT: G 14 LYS cc_start: 0.7563 (ptmt) cc_final: 0.7204 (ptmt) REVERT: G 16 VAL cc_start: 0.8076 (t) cc_final: 0.7839 (p) REVERT: G 20 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7813 (mtmm) outliers start: 8 outliers final: 3 residues processed: 230 average time/residue: 0.1211 time to fit residues: 36.2519 Evaluate side-chains 173 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS R 194 ASN R 257 GLN A 19 GLN A 220 HIS A 278 ASN B 44 GLN B 75 GLN B 88 ASN N 3 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089587 restraints weight = 16168.727| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.67 r_work: 0.3046 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9223 Z= 0.222 Angle : 0.611 7.699 12508 Z= 0.327 Chirality : 0.044 0.163 1391 Planarity : 0.005 0.077 1599 Dihedral : 4.043 19.731 1250 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.37 % Allowed : 20.44 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1132 helix: 1.86 (0.25), residues: 449 sheet: -0.64 (0.33), residues: 238 loop : -0.83 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.012 0.001 TYR R 150 PHE 0.027 0.002 PHE R 119 TRP 0.026 0.002 TRP R 82 HIS 0.004 0.001 HIS R 201 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 9215) covalent geometry : angle 0.61012 (12494) SS BOND : bond 0.00491 ( 7) SS BOND : angle 1.19828 ( 14) hydrogen bonds : bond 0.04804 ( 437) hydrogen bonds : angle 4.86108 ( 1254) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 82 TRP cc_start: 0.5946 (m100) cc_final: 0.5027 (m-10) REVERT: B 13 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8302 (mm-40) REVERT: B 59 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8617 (m-80) REVERT: B 173 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 258 ASP cc_start: 0.7956 (t0) cc_final: 0.7586 (t0) REVERT: G 16 VAL cc_start: 0.9122 (t) cc_final: 0.8833 (p) REVERT: G 20 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8267 (mtmm) outliers start: 51 outliers final: 25 residues processed: 204 average time/residue: 0.0943 time to fit residues: 26.3642 Evaluate side-chains 185 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 392 CYS Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.127790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.096411 restraints weight = 16905.338| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.86 r_work: 0.3230 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9223 Z= 0.136 Angle : 0.525 7.375 12508 Z= 0.283 Chirality : 0.042 0.146 1391 Planarity : 0.004 0.058 1599 Dihedral : 3.865 19.329 1247 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.06 % Allowed : 22.44 % 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: 0.54 (0.26), residues: 1132 helix: 2.10 (0.25), residues: 449 sheet: -0.67 (0.32), residues: 250 loop : -0.84 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.012 0.001 TYR N 80 PHE 0.010 0.001 PHE R 224 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9215) covalent geometry : angle 0.52274 (12494) SS BOND : bond 0.00348 ( 7) SS BOND : angle 1.40782 ( 14) hydrogen bonds : bond 0.04110 ( 437) hydrogen bonds : angle 4.54898 ( 1254) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 82 TRP cc_start: 0.5811 (m100) cc_final: 0.5308 (m-10) REVERT: R 373 ASP cc_start: 0.8711 (p0) cc_final: 0.8391 (p0) REVERT: A 317 ARG cc_start: 0.8613 (tpp80) cc_final: 0.8056 (tmm160) REVERT: B 13 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8333 (mm-40) REVERT: B 59 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.8584 (m-80) REVERT: B 173 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8596 (m) REVERT: B 258 ASP cc_start: 0.8065 (t0) cc_final: 0.7546 (t0) REVERT: G 16 VAL cc_start: 0.9166 (t) cc_final: 0.8790 (p) REVERT: G 17 GLU cc_start: 0.8546 (pp20) cc_final: 0.8198 (pp20) REVERT: G 20 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8288 (mtmm) REVERT: N 46 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7266 (mm-30) REVERT: N 88 PRO cc_start: 0.8561 (Cg_exo) cc_final: 0.8354 (Cg_endo) outliers start: 29 outliers final: 19 residues processed: 196 average time/residue: 0.1081 time to fit residues: 28.6175 Evaluate side-chains 181 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.123768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092960 restraints weight = 16750.856| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.83 r_work: 0.3182 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9223 Z= 0.167 Angle : 0.544 7.573 12508 Z= 0.291 Chirality : 0.042 0.142 1391 Planarity : 0.004 0.049 1599 Dihedral : 3.948 17.057 1247 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.85 % Allowed : 22.13 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.26), residues: 1132 helix: 2.08 (0.25), residues: 448 sheet: -0.78 (0.32), residues: 245 loop : -0.82 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 38 TYR 0.013 0.001 TYR N 60 PHE 0.012 0.001 PHE N 108 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.001 HIS R 201 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9215) covalent geometry : angle 0.54135 (12494) SS BOND : bond 0.00337 ( 7) SS BOND : angle 1.71140 ( 14) hydrogen bonds : bond 0.03986 ( 437) hydrogen bonds : angle 4.45657 ( 1254) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 82 TRP cc_start: 0.6002 (m100) cc_final: 0.5184 (m-10) REVERT: R 373 ASP cc_start: 0.8654 (p0) cc_final: 0.8323 (p0) REVERT: R 408 GLN cc_start: 0.7508 (mp10) cc_final: 0.7046 (mp10) REVERT: A 317 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8068 (tmm160) REVERT: B 13 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8434 (mm-40) REVERT: B 59 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: B 173 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8705 (m) REVERT: B 258 ASP cc_start: 0.8104 (t0) cc_final: 0.7664 (t0) REVERT: G 17 GLU cc_start: 0.8606 (pp20) cc_final: 0.8236 (pp20) REVERT: G 20 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8316 (mtmm) REVERT: N 46 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7226 (mm-30) outliers start: 46 outliers final: 32 residues processed: 205 average time/residue: 0.1016 time to fit residues: 28.7035 Evaluate side-chains 189 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 7 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 0.0770 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 39 optimal weight: 6.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094465 restraints weight = 16748.139| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.85 r_work: 0.3210 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9223 Z= 0.119 Angle : 0.525 8.267 12508 Z= 0.280 Chirality : 0.041 0.142 1391 Planarity : 0.003 0.043 1599 Dihedral : 3.855 18.322 1247 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.43 % Allowed : 22.02 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1132 helix: 2.12 (0.25), residues: 448 sheet: -0.74 (0.32), residues: 243 loop : -0.73 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.011 0.001 TYR N 80 PHE 0.011 0.001 PHE R 224 TRP 0.018 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9215) covalent geometry : angle 0.52063 (12494) SS BOND : bond 0.00418 ( 7) SS BOND : angle 2.02433 ( 14) hydrogen bonds : bond 0.03620 ( 437) hydrogen bonds : angle 4.32349 ( 1254) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 373 ASP cc_start: 0.8604 (p0) cc_final: 0.8291 (p0) REVERT: R 408 GLN cc_start: 0.7429 (mt0) cc_final: 0.7015 (mp10) REVERT: A 317 ARG cc_start: 0.8669 (tpp80) cc_final: 0.8132 (tmm160) REVERT: B 13 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8467 (mm-40) REVERT: B 59 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8656 (m-80) REVERT: B 258 ASP cc_start: 0.8139 (t0) cc_final: 0.7696 (t0) REVERT: G 17 GLU cc_start: 0.8650 (pp20) cc_final: 0.8334 (pp20) REVERT: G 20 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8344 (mtmm) REVERT: G 26 ASP cc_start: 0.8394 (t0) cc_final: 0.8165 (t0) REVERT: N 46 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7173 (mm-30) outliers start: 42 outliers final: 32 residues processed: 210 average time/residue: 0.0957 time to fit residues: 27.6177 Evaluate side-chains 192 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 19 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093716 restraints weight = 16817.721| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.88 r_work: 0.3211 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9223 Z= 0.119 Angle : 0.525 7.622 12508 Z= 0.281 Chirality : 0.041 0.149 1391 Planarity : 0.003 0.042 1599 Dihedral : 3.876 19.160 1247 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.53 % Allowed : 22.44 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.26), residues: 1132 helix: 2.19 (0.25), residues: 447 sheet: -0.67 (0.32), residues: 248 loop : -0.78 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 38 TYR 0.012 0.001 TYR N 80 PHE 0.011 0.001 PHE R 224 TRP 0.021 0.001 TRP R 118 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9215) covalent geometry : angle 0.51756 (12494) SS BOND : bond 0.00394 ( 7) SS BOND : angle 2.74469 ( 14) hydrogen bonds : bond 0.03519 ( 437) hydrogen bonds : angle 4.25069 ( 1254) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 101 ASP cc_start: 0.7687 (t0) cc_final: 0.7341 (t0) REVERT: R 211 LEU cc_start: 0.7681 (mt) cc_final: 0.7439 (mt) REVERT: R 373 ASP cc_start: 0.8588 (p0) cc_final: 0.8275 (p0) REVERT: R 408 GLN cc_start: 0.7393 (mt0) cc_final: 0.6982 (mp10) REVERT: A 317 ARG cc_start: 0.8653 (tpp80) cc_final: 0.7788 (tmm160) REVERT: B 13 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8456 (mm-40) REVERT: B 59 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: B 258 ASP cc_start: 0.8121 (t0) cc_final: 0.7672 (t0) REVERT: G 17 GLU cc_start: 0.8627 (pp20) cc_final: 0.8328 (pp20) REVERT: G 20 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8349 (mtmm) REVERT: N 46 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7182 (mm-30) REVERT: N 127 SER cc_start: 0.6876 (OUTLIER) cc_final: 0.6620 (p) outliers start: 43 outliers final: 37 residues processed: 202 average time/residue: 0.0946 time to fit residues: 26.6165 Evaluate side-chains 199 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 107 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.124577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093658 restraints weight = 16954.359| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.92 r_work: 0.3217 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9223 Z= 0.117 Angle : 0.526 7.701 12508 Z= 0.281 Chirality : 0.041 0.152 1391 Planarity : 0.003 0.041 1599 Dihedral : 3.904 19.597 1247 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.21 % Allowed : 23.50 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1132 helix: 2.27 (0.25), residues: 442 sheet: -0.63 (0.32), residues: 243 loop : -0.78 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.013 0.001 TYR N 80 PHE 0.011 0.001 PHE R 224 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9215) covalent geometry : angle 0.52342 (12494) SS BOND : bond 0.00320 ( 7) SS BOND : angle 1.50274 ( 14) hydrogen bonds : bond 0.03481 ( 437) hydrogen bonds : angle 4.21684 ( 1254) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 82 TRP cc_start: 0.5938 (m100) cc_final: 0.5230 (m-10) REVERT: R 211 LEU cc_start: 0.7659 (mt) cc_final: 0.7381 (mt) REVERT: R 373 ASP cc_start: 0.8580 (p0) cc_final: 0.8262 (p0) REVERT: A 317 ARG cc_start: 0.8657 (tpp80) cc_final: 0.7814 (tmm160) REVERT: B 13 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8478 (mm-40) REVERT: B 59 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8624 (m-80) REVERT: B 258 ASP cc_start: 0.8112 (t0) cc_final: 0.7724 (t0) REVERT: G 17 GLU cc_start: 0.8633 (pp20) cc_final: 0.8360 (pp20) REVERT: G 20 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8411 (mtmm) REVERT: N 46 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7167 (mm-30) REVERT: N 74 ASN cc_start: 0.8032 (p0) cc_final: 0.7762 (m-40) REVERT: N 127 SER cc_start: 0.6839 (OUTLIER) cc_final: 0.6569 (p) outliers start: 40 outliers final: 36 residues processed: 207 average time/residue: 0.0940 time to fit residues: 26.9516 Evaluate side-chains 200 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.124293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093405 restraints weight = 16934.843| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.92 r_work: 0.3211 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9223 Z= 0.119 Angle : 0.545 13.233 12508 Z= 0.284 Chirality : 0.041 0.162 1391 Planarity : 0.004 0.041 1599 Dihedral : 3.857 20.298 1247 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.43 % Allowed : 23.50 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1132 helix: 2.29 (0.25), residues: 447 sheet: -0.60 (0.32), residues: 248 loop : -0.78 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.014 0.001 TYR N 80 PHE 0.010 0.001 PHE R 224 TRP 0.020 0.001 TRP R 118 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9215) covalent geometry : angle 0.54160 (12494) SS BOND : bond 0.00367 ( 7) SS BOND : angle 1.87330 ( 14) hydrogen bonds : bond 0.03402 ( 437) hydrogen bonds : angle 4.13707 ( 1254) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 LEU cc_start: 0.7657 (mt) cc_final: 0.7411 (mt) REVERT: R 373 ASP cc_start: 0.8570 (p0) cc_final: 0.8283 (p0) REVERT: R 408 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6724 (mt0) REVERT: B 13 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8527 (mm-40) REVERT: B 59 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8674 (m-80) REVERT: B 258 ASP cc_start: 0.8089 (t0) cc_final: 0.7737 (t0) REVERT: G 17 GLU cc_start: 0.8637 (pp20) cc_final: 0.8385 (pp20) REVERT: G 20 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8414 (mtmm) REVERT: G 22 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8084 (mp0) REVERT: N 46 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7178 (mm-30) REVERT: N 127 SER cc_start: 0.6861 (OUTLIER) cc_final: 0.6584 (p) outliers start: 42 outliers final: 37 residues processed: 204 average time/residue: 0.0890 time to fit residues: 25.6797 Evaluate side-chains 203 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 338 TYR Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.0170 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.125149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094524 restraints weight = 16949.683| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.92 r_work: 0.3222 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9223 Z= 0.121 Angle : 0.558 12.604 12508 Z= 0.291 Chirality : 0.041 0.164 1391 Planarity : 0.004 0.041 1599 Dihedral : 3.822 21.207 1247 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.43 % Allowed : 23.50 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.26), residues: 1132 helix: 2.35 (0.25), residues: 444 sheet: -0.64 (0.32), residues: 243 loop : -0.74 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.014 0.001 TYR N 80 PHE 0.010 0.001 PHE R 224 TRP 0.026 0.001 TRP R 118 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9215) covalent geometry : angle 0.55516 (12494) SS BOND : bond 0.00350 ( 7) SS BOND : angle 1.64321 ( 14) hydrogen bonds : bond 0.03386 ( 437) hydrogen bonds : angle 4.08946 ( 1254) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 LEU cc_start: 0.7670 (mt) cc_final: 0.7422 (mt) REVERT: R 373 ASP cc_start: 0.8554 (p0) cc_final: 0.8259 (p0) REVERT: R 408 GLN cc_start: 0.7170 (tm-30) cc_final: 0.6807 (mt0) REVERT: B 13 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8548 (mm-40) REVERT: B 59 TYR cc_start: 0.9131 (OUTLIER) cc_final: 0.8677 (m-80) REVERT: B 258 ASP cc_start: 0.8110 (t0) cc_final: 0.7756 (t0) REVERT: G 17 GLU cc_start: 0.8624 (pp20) cc_final: 0.8411 (pp20) REVERT: G 20 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8447 (mtmm) REVERT: G 22 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8098 (mp0) REVERT: N 46 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7181 (mm-30) REVERT: N 127 SER cc_start: 0.6857 (OUTLIER) cc_final: 0.6583 (p) outliers start: 42 outliers final: 36 residues processed: 204 average time/residue: 0.0949 time to fit residues: 27.2277 Evaluate side-chains 201 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 0.0370 chunk 92 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 31 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099064 restraints weight = 16901.997| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.93 r_work: 0.3291 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9223 Z= 0.112 Angle : 0.566 11.720 12508 Z= 0.296 Chirality : 0.041 0.164 1391 Planarity : 0.004 0.041 1599 Dihedral : 3.783 19.003 1247 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.69 % Allowed : 24.97 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1132 helix: 2.40 (0.25), residues: 444 sheet: -0.61 (0.32), residues: 243 loop : -0.81 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.014 0.001 TYR N 80 PHE 0.020 0.001 PHE R 161 TRP 0.038 0.001 TRP R 118 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9215) covalent geometry : angle 0.56398 (12494) SS BOND : bond 0.00335 ( 7) SS BOND : angle 1.45644 ( 14) hydrogen bonds : bond 0.03223 ( 437) hydrogen bonds : angle 4.03563 ( 1254) Misc. bond : bond 0.00011 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 211 LEU cc_start: 0.7669 (mt) cc_final: 0.7421 (mt) REVERT: R 373 ASP cc_start: 0.8528 (p0) cc_final: 0.8233 (p0) REVERT: R 408 GLN cc_start: 0.7246 (tm-30) cc_final: 0.6823 (mt0) REVERT: B 13 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8387 (mm-40) REVERT: B 59 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: B 258 ASP cc_start: 0.8015 (t0) cc_final: 0.7668 (t0) REVERT: G 20 LYS cc_start: 0.8842 (mtmm) cc_final: 0.8483 (mtmm) REVERT: G 22 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8093 (mp0) REVERT: N 46 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7208 (mm-30) REVERT: N 74 ASN cc_start: 0.8125 (p0) cc_final: 0.7743 (m-40) REVERT: N 98 ARG cc_start: 0.8814 (tmm-80) cc_final: 0.8613 (ttp80) REVERT: N 127 SER cc_start: 0.6868 (OUTLIER) cc_final: 0.6590 (p) outliers start: 35 outliers final: 32 residues processed: 198 average time/residue: 0.0972 time to fit residues: 26.9460 Evaluate side-chains 198 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 TRP Chi-restraints excluded: chain R residue 147 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 287 ASP Chi-restraints excluded: chain R residue 334 GLU Chi-restraints excluded: chain R residue 354 ILE Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.129306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098325 restraints weight = 16520.251| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.91 r_work: 0.3289 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9223 Z= 0.133 Angle : 0.573 11.519 12508 Z= 0.301 Chirality : 0.041 0.167 1391 Planarity : 0.004 0.041 1599 Dihedral : 3.789 19.631 1247 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.32 % Allowed : 24.55 % Favored : 71.13 % 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: 0.72 (0.26), residues: 1132 helix: 2.39 (0.25), residues: 444 sheet: -0.69 (0.32), residues: 244 loop : -0.79 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.013 0.001 TYR N 80 PHE 0.011 0.001 PHE N 108 TRP 0.036 0.001 TRP R 118 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9215) covalent geometry : angle 0.57092 (12494) SS BOND : bond 0.00311 ( 7) SS BOND : angle 1.45092 ( 14) hydrogen bonds : bond 0.03384 ( 437) hydrogen bonds : angle 4.04180 ( 1254) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.74 seconds wall clock time: 37 minutes 10.05 seconds (2230.05 seconds total)