Starting phenix.real_space_refine on Wed Sep 17 11:29:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5y_44229/09_2025/9b5y_44229.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5y_44229/09_2025/9b5y_44229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b5y_44229/09_2025/9b5y_44229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5y_44229/09_2025/9b5y_44229.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b5y_44229/09_2025/9b5y_44229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5y_44229/09_2025/9b5y_44229.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 49 5.16 5 C 5370 2.51 5 N 1441 2.21 5 O 1569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 8429 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1844 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 4, 'TRANS': 244} Chain breaks: 3 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 8, 'ASP:plan': 2, 'TYR:plan': 3, 'PHE:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 120 Chain: "A" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1607 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 9, 'PHE:plan': 3, 'GLN:plan1': 4, 'TYR:plan': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 169 Chain: "L" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 179 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "N" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1770 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 2.15, per 1000 atoms: 0.26 Number of scatterers: 8429 At special positions: 0 Unit cell: (89.424, 122.544, 133.308, 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 49 16.00 O 1569 8.00 N 1441 7.00 C 5370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 520.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 35.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.828A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA R 205 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 244 Processing helix chain 'R' and resid 280 through 310 removed outlier: 3.667A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 322 removed outlier: 4.000A pdb=" N LEU R 321 " --> pdb=" O GLU R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 339 removed outlier: 3.608A pdb=" N VAL R 326 " --> pdb=" O TRP R 322 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE R 327 " --> pdb=" O GLY R 323 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.602A pdb=" N PHE R 335 " --> pdb=" O LEU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 391 removed outlier: 3.530A pdb=" N THR R 387 " --> pdb=" O ARG R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 403 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 434 through 445 Processing helix chain 'R' and resid 455 through 460 Processing helix chain 'R' and resid 465 through 470 Processing helix chain 'A' and resid 12 through 35 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.522A pdb=" N GLU A 221 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN A 222 " --> pdb=" O CYS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.520A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.669A pdb=" N ALA A 302 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.963A pdb=" N LEU A 316 " --> pdb=" O MET A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'L' and resid 2 through 21 removed outlier: 3.686A pdb=" N ARG L 19 " --> pdb=" O ILE L 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.594A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.838A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.783A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.815A pdb=" N ASP N 90 " --> pdb=" O ARG N 87 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'N' and resid 221 through 225 removed outlier: 3.891A pdb=" N VAL N 225 " --> pdb=" O ALA N 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.818A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'G' and resid 44 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 206 removed outlier: 6.258A pdb=" N LEU A 40 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 206 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU A 42 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 230 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 50 removed outlier: 3.725A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.988A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.882A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.295A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.576A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.594A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.766A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.518A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.863A pdb=" N VAL N 97 " --> pdb=" O HIS N 35 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N MET N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 4.434A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 147 through 149 removed outlier: 6.409A pdb=" N VAL N 148 " --> pdb=" O GLU N 247 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 190 " --> pdb=" O TRP N 177 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU N 188 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 156 through 157 removed outlier: 3.584A pdb=" N CYS N 160 " --> pdb=" O PHE N 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 156 through 157 removed outlier: 3.668A pdb=" N SER N 207 " --> pdb=" O THR N 214 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1071 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: 1.40 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1977 1.33 - 1.45: 1852 1.45 - 1.57: 4699 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8600 Sorted by residual: bond pdb=" N LEU R 331 " pdb=" CA LEU R 331 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.30e+01 bond pdb=" N GLY N 241 " pdb=" CA GLY N 241 " ideal model delta sigma weight residual 1.445 1.470 -0.026 9.90e-03 1.02e+04 6.73e+00 bond pdb=" CA SER R 308 " pdb=" CB SER R 308 " ideal model delta sigma weight residual 1.536 1.484 0.052 2.01e-02 2.48e+03 6.58e+00 bond pdb=" N PHE R 327 " pdb=" CA PHE R 327 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.32e+00 bond pdb=" N LEU R 306 " pdb=" CA LEU R 306 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.15e+00 ... (remaining 8595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 11644 4.34 - 8.67: 43 8.67 - 13.01: 3 13.01 - 17.35: 2 17.35 - 21.68: 2 Bond angle restraints: 11694 Sorted by residual: angle pdb=" C PRO N 14 " pdb=" CA PRO N 14 " pdb=" CB PRO N 14 " ideal model delta sigma weight residual 111.23 129.61 -18.38 1.28e+00 6.10e-01 2.06e+02 angle pdb=" N PRO N 14 " pdb=" CA PRO N 14 " pdb=" C PRO N 14 " ideal model delta sigma weight residual 111.21 89.53 21.68 1.59e+00 3.96e-01 1.86e+02 angle pdb=" N GLY N 15 " pdb=" CA GLY N 15 " pdb=" C GLY N 15 " ideal model delta sigma weight residual 115.59 130.96 -15.37 1.32e+00 5.74e-01 1.36e+02 angle pdb=" N PRO N 237 " pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 112.47 96.26 16.21 2.06e+00 2.36e-01 6.19e+01 angle pdb=" N LEU N 238 " pdb=" CA LEU N 238 " pdb=" C LEU N 238 " ideal model delta sigma weight residual 109.71 99.47 10.24 1.41e+00 5.03e-01 5.28e+01 ... (remaining 11689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 4240 14.62 - 29.23: 508 29.23 - 43.85: 216 43.85 - 58.46: 66 58.46 - 73.08: 14 Dihedral angle restraints: 5044 sinusoidal: 1787 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 162.73 -69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 29.61 63.39 1 1.00e+01 1.00e-02 5.30e+01 dihedral pdb=" C GLU N 235 " pdb=" N GLU N 235 " pdb=" CA GLU N 235 " pdb=" CB GLU N 235 " ideal model delta harmonic sigma weight residual -122.60 -135.54 12.94 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 5041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1166 0.062 - 0.125: 174 0.125 - 0.187: 10 0.187 - 0.249: 4 0.249 - 0.311: 5 Chirality restraints: 1359 Sorted by residual: chirality pdb=" CA LEU N 238 " pdb=" N LEU N 238 " pdb=" C LEU N 238 " pdb=" CB LEU N 238 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA GLU N 235 " pdb=" N GLU N 235 " pdb=" C GLU N 235 " pdb=" CB GLU N 235 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA TYR N 236 " pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CB TYR N 236 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1356 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 324 " -0.023 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE R 324 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 324 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE R 324 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE R 324 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 324 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE R 324 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 319 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C LYS R 319 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS R 319 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR R 320 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 306 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C LEU R 306 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU R 306 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS R 307 " -0.017 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1484 2.76 - 3.30: 7895 3.30 - 3.83: 14155 3.83 - 4.37: 15963 4.37 - 4.90: 28030 Nonbonded interactions: 67527 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O SER B 160 " model vdw 2.230 3.040 nonbonded pdb=" O GLU R 444 " pdb=" ND2 ASN R 448 " model vdw 2.249 3.120 nonbonded pdb=" NE2 GLN N 232 " pdb=" O PRO N 237 " model vdw 2.253 3.120 nonbonded pdb=" N PRO N 14 " pdb=" O PRO N 14 " model vdw 2.261 2.496 nonbonded pdb=" ND2 ASN A 317 " pdb=" OD1 ASP A 319 " model vdw 2.304 3.120 ... (remaining 67522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 9.750 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 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 : 0.004 0.052 8603 Z= 0.234 Angle : 0.777 21.681 11700 Z= 0.484 Chirality : 0.048 0.311 1359 Planarity : 0.004 0.048 1485 Dihedral : 16.505 73.078 2929 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.30 % Allowed : 28.57 % Favored : 70.13 % Cbeta Deviations : 0.19 % 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: -0.53 (0.27), residues: 1103 helix: 1.49 (0.29), residues: 360 sheet: -0.95 (0.32), residues: 289 loop : -1.42 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.031 0.002 TYR R 191 PHE 0.057 0.002 PHE R 324 TRP 0.043 0.002 TRP B 82 HIS 0.009 0.001 HIS R 307 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8600) covalent geometry : angle 0.77667 (11694) SS BOND : bond 0.00169 ( 3) SS BOND : angle 0.68165 ( 6) hydrogen bonds : bond 0.17761 ( 371) hydrogen bonds : angle 7.20927 ( 1071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.307 Fit side-chains REVERT: A 26 ASP cc_start: 0.7329 (t0) cc_final: 0.6970 (m-30) REVERT: B 258 ASP cc_start: 0.6505 (t0) cc_final: 0.5870 (t0) REVERT: N 192 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7291 (mtm180) outliers start: 11 outliers final: 5 residues processed: 147 average time/residue: 0.0906 time to fit residues: 18.9057 Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 319 ASP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 234 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS R 295 ASN A 317 ASN B 88 ASN N 39 GLN G 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.149326 restraints weight = 11366.562| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.77 r_work: 0.3700 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.185 Angle : 0.562 7.350 11700 Z= 0.303 Chirality : 0.042 0.154 1359 Planarity : 0.004 0.053 1485 Dihedral : 4.923 44.050 1210 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.60 % Allowed : 24.32 % Favored : 71.07 % 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: -0.47 (0.27), residues: 1103 helix: 1.55 (0.29), residues: 369 sheet: -0.87 (0.31), residues: 299 loop : -1.49 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 314 TYR 0.021 0.002 TYR R 191 PHE 0.059 0.002 PHE R 324 TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8600) covalent geometry : angle 0.56156 (11694) SS BOND : bond 0.00265 ( 3) SS BOND : angle 0.67720 ( 6) hydrogen bonds : bond 0.04143 ( 371) hydrogen bonds : angle 4.93833 ( 1071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.397 Fit side-chains REVERT: R 457 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8142 (tp) REVERT: B 49 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7240 (mtt-85) REVERT: B 83 ASP cc_start: 0.8097 (t0) cc_final: 0.7756 (t70) REVERT: B 129 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7352 (mtt90) REVERT: B 159 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7338 (p) REVERT: N 18 ARG cc_start: 0.6436 (ttt180) cc_final: 0.6197 (ttt180) REVERT: N 89 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6193 (pp20) outliers start: 39 outliers final: 18 residues processed: 176 average time/residue: 0.0934 time to fit residues: 23.1560 Evaluate side-chains 173 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 234 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 89 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 223 HIS ** R 442 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 = 0.4126 r_free = 0.4126 target = 0.172103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148710 restraints weight = 11297.988| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.75 r_work: 0.3732 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8603 Z= 0.150 Angle : 0.523 6.415 11700 Z= 0.280 Chirality : 0.040 0.148 1359 Planarity : 0.004 0.051 1485 Dihedral : 4.747 45.261 1207 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.19 % Allowed : 24.79 % Favored : 70.01 % 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: -0.34 (0.26), residues: 1103 helix: 1.75 (0.29), residues: 366 sheet: -0.80 (0.31), residues: 291 loop : -1.48 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.019 0.001 TYR R 191 PHE 0.032 0.002 PHE R 324 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8600) covalent geometry : angle 0.52312 (11694) SS BOND : bond 0.00311 ( 3) SS BOND : angle 0.57508 ( 6) hydrogen bonds : bond 0.03730 ( 371) hydrogen bonds : angle 4.65491 ( 1071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.285 Fit side-chains REVERT: R 457 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8045 (tp) REVERT: A 356 TYR cc_start: 0.5368 (OUTLIER) cc_final: 0.4997 (t80) REVERT: B 49 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7212 (mtt-85) REVERT: B 83 ASP cc_start: 0.8119 (t0) cc_final: 0.7313 (t0) REVERT: B 159 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7283 (p) REVERT: B 247 ASP cc_start: 0.7939 (p0) cc_final: 0.7728 (p0) REVERT: B 280 LYS cc_start: 0.8386 (tttt) cc_final: 0.8142 (tttm) REVERT: N 89 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6250 (pp20) outliers start: 44 outliers final: 26 residues processed: 173 average time/residue: 0.0897 time to fit residues: 21.8822 Evaluate side-chains 176 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 325 THR Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.173707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149670 restraints weight = 11453.809| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.85 r_work: 0.3717 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8603 Z= 0.142 Angle : 0.515 6.720 11700 Z= 0.274 Chirality : 0.040 0.144 1359 Planarity : 0.004 0.050 1485 Dihedral : 4.717 46.436 1207 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.08 % Allowed : 25.97 % Favored : 68.95 % 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: -0.31 (0.26), residues: 1103 helix: 1.75 (0.29), residues: 368 sheet: -0.80 (0.31), residues: 289 loop : -1.45 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.020 0.001 TYR R 191 PHE 0.027 0.001 PHE R 324 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8600) covalent geometry : angle 0.51516 (11694) SS BOND : bond 0.00284 ( 3) SS BOND : angle 0.67150 ( 6) hydrogen bonds : bond 0.03486 ( 371) hydrogen bonds : angle 4.49154 ( 1071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.316 Fit side-chains REVERT: R 421 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.5846 (p90) REVERT: R 457 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8053 (tp) REVERT: A 356 TYR cc_start: 0.5414 (OUTLIER) cc_final: 0.5016 (t80) REVERT: B 49 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7135 (mtt-85) REVERT: B 83 ASP cc_start: 0.8110 (t0) cc_final: 0.7334 (t0) REVERT: B 149 CYS cc_start: 0.7428 (p) cc_final: 0.7219 (m) REVERT: B 247 ASP cc_start: 0.7883 (p0) cc_final: 0.7645 (p0) outliers start: 43 outliers final: 28 residues processed: 181 average time/residue: 0.0858 time to fit residues: 22.2601 Evaluate side-chains 185 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 98 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 374 ASN ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.169874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145794 restraints weight = 11315.494| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.82 r_work: 0.3656 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8603 Z= 0.265 Angle : 0.604 6.740 11700 Z= 0.321 Chirality : 0.044 0.185 1359 Planarity : 0.004 0.053 1485 Dihedral : 5.203 49.590 1207 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 6.14 % Allowed : 25.97 % Favored : 67.89 % 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: -0.59 (0.26), residues: 1103 helix: 1.35 (0.28), residues: 376 sheet: -1.04 (0.30), residues: 295 loop : -1.41 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.025 0.002 TYR R 191 PHE 0.030 0.002 PHE R 324 TRP 0.019 0.002 TRP B 169 HIS 0.006 0.002 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00614 ( 8600) covalent geometry : angle 0.60368 (11694) SS BOND : bond 0.00382 ( 3) SS BOND : angle 0.69381 ( 6) hydrogen bonds : bond 0.04056 ( 371) hydrogen bonds : angle 4.78633 ( 1071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.317 Fit side-chains REVERT: R 421 TYR cc_start: 0.6403 (OUTLIER) cc_final: 0.5552 (p90) REVERT: R 457 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8180 (tp) REVERT: A 356 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5089 (t80) REVERT: B 49 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7166 (mtt-85) REVERT: B 83 ASP cc_start: 0.8162 (t0) cc_final: 0.7535 (t0) REVERT: B 247 ASP cc_start: 0.7943 (p0) cc_final: 0.7723 (p0) REVERT: N 18 ARG cc_start: 0.6849 (ttt180) cc_final: 0.6563 (ttt180) outliers start: 52 outliers final: 37 residues processed: 185 average time/residue: 0.0893 time to fit residues: 23.3472 Evaluate side-chains 192 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 221 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 237 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.171502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.148196 restraints weight = 11333.870| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.74 r_work: 0.3691 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.181 Angle : 0.550 6.942 11700 Z= 0.292 Chirality : 0.041 0.169 1359 Planarity : 0.004 0.056 1485 Dihedral : 4.986 47.471 1207 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.19 % Allowed : 27.63 % Favored : 67.18 % 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: -0.48 (0.26), residues: 1103 helix: 1.48 (0.29), residues: 373 sheet: -0.91 (0.32), residues: 274 loop : -1.44 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.025 0.002 TYR R 191 PHE 0.023 0.002 PHE R 324 TRP 0.018 0.002 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8600) covalent geometry : angle 0.55036 (11694) SS BOND : bond 0.00308 ( 3) SS BOND : angle 0.54826 ( 6) hydrogen bonds : bond 0.03618 ( 371) hydrogen bonds : angle 4.58913 ( 1071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.231 Fit side-chains REVERT: R 421 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.5875 (p90) REVERT: A 271 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7911 (tp) REVERT: A 356 TYR cc_start: 0.5315 (OUTLIER) cc_final: 0.4974 (t80) REVERT: B 49 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7052 (mtt-85) REVERT: B 83 ASP cc_start: 0.8119 (t0) cc_final: 0.7438 (t0) REVERT: B 247 ASP cc_start: 0.7880 (p0) cc_final: 0.7659 (p0) REVERT: N 18 ARG cc_start: 0.6633 (ttt180) cc_final: 0.6369 (ttt180) REVERT: N 52 SER cc_start: 0.8059 (m) cc_final: 0.7695 (t) REVERT: N 89 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6366 (pp20) outliers start: 44 outliers final: 35 residues processed: 182 average time/residue: 0.0888 time to fit residues: 22.6667 Evaluate side-chains 193 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 34 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.173414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150008 restraints weight = 11468.236| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.77 r_work: 0.3706 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8603 Z= 0.131 Angle : 0.516 7.286 11700 Z= 0.272 Chirality : 0.040 0.147 1359 Planarity : 0.004 0.053 1485 Dihedral : 4.726 44.974 1207 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.43 % Allowed : 27.27 % Favored : 67.30 % 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: -0.37 (0.26), residues: 1103 helix: 1.70 (0.29), residues: 369 sheet: -0.84 (0.31), residues: 287 loop : -1.47 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.023 0.001 TYR R 191 PHE 0.018 0.001 PHE R 324 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8600) covalent geometry : angle 0.51625 (11694) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.59539 ( 6) hydrogen bonds : bond 0.03279 ( 371) hydrogen bonds : angle 4.36154 ( 1071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 0.323 Fit side-chains REVERT: R 421 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5776 (p90) REVERT: A 271 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7831 (tp) REVERT: A 356 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.4983 (t80) REVERT: B 49 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6928 (mtt-85) REVERT: B 83 ASP cc_start: 0.8082 (t0) cc_final: 0.7640 (t0) REVERT: B 110 ASN cc_start: 0.8299 (m-40) cc_final: 0.7995 (m-40) REVERT: B 247 ASP cc_start: 0.7816 (p0) cc_final: 0.7592 (p0) REVERT: B 280 LYS cc_start: 0.8424 (tttp) cc_final: 0.8219 (tttm) REVERT: N 52 SER cc_start: 0.8052 (m) cc_final: 0.7687 (t) REVERT: N 89 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6393 (pp20) outliers start: 46 outliers final: 33 residues processed: 178 average time/residue: 0.0849 time to fit residues: 21.7208 Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 11 optimal weight: 0.0970 chunk 88 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN B 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.145900 restraints weight = 11375.843| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.86 r_work: 0.3688 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8603 Z= 0.163 Angle : 0.552 10.999 11700 Z= 0.285 Chirality : 0.041 0.133 1359 Planarity : 0.004 0.054 1485 Dihedral : 4.808 45.024 1207 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.72 % Allowed : 28.45 % Favored : 66.82 % 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: -0.38 (0.26), residues: 1103 helix: 1.64 (0.29), residues: 371 sheet: -0.82 (0.32), residues: 287 loop : -1.48 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.021 0.001 TYR R 191 PHE 0.020 0.002 PHE R 324 TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8600) covalent geometry : angle 0.55154 (11694) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.55424 ( 6) hydrogen bonds : bond 0.03409 ( 371) hydrogen bonds : angle 4.42260 ( 1071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.233 Fit side-chains REVERT: R 192 THR cc_start: 0.7985 (m) cc_final: 0.7710 (m) REVERT: R 226 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5632 (tt) REVERT: R 421 TYR cc_start: 0.6464 (OUTLIER) cc_final: 0.5827 (p90) REVERT: A 271 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7816 (tp) REVERT: B 49 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7012 (mtt-85) REVERT: B 83 ASP cc_start: 0.8123 (t0) cc_final: 0.7717 (t0) REVERT: B 247 ASP cc_start: 0.7856 (p0) cc_final: 0.7654 (p0) REVERT: N 52 SER cc_start: 0.8068 (m) cc_final: 0.7721 (t) outliers start: 40 outliers final: 34 residues processed: 171 average time/residue: 0.0816 time to fit residues: 19.9885 Evaluate side-chains 186 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 HIS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 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 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.172766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149437 restraints weight = 11334.748| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.75 r_work: 0.3711 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.152 Angle : 0.539 7.361 11700 Z= 0.283 Chirality : 0.041 0.133 1359 Planarity : 0.004 0.054 1485 Dihedral : 4.766 44.940 1207 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.84 % Allowed : 28.34 % Favored : 66.82 % 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: -0.36 (0.26), residues: 1103 helix: 1.68 (0.29), residues: 369 sheet: -0.79 (0.32), residues: 287 loop : -1.48 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.021 0.002 TYR R 191 PHE 0.029 0.001 PHE R 324 TRP 0.017 0.001 TRP B 169 HIS 0.006 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8600) covalent geometry : angle 0.53866 (11694) SS BOND : bond 0.00282 ( 3) SS BOND : angle 0.59487 ( 6) hydrogen bonds : bond 0.03379 ( 371) hydrogen bonds : angle 4.37509 ( 1071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.327 Fit side-chains REVERT: R 192 THR cc_start: 0.7967 (m) cc_final: 0.7689 (m) REVERT: R 226 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5548 (tt) REVERT: R 421 TYR cc_start: 0.6496 (OUTLIER) cc_final: 0.5863 (p90) REVERT: A 271 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 49 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6942 (mtt-85) REVERT: B 83 ASP cc_start: 0.8099 (t0) cc_final: 0.7680 (t0) REVERT: N 52 SER cc_start: 0.8060 (m) cc_final: 0.7706 (t) outliers start: 41 outliers final: 36 residues processed: 172 average time/residue: 0.0811 time to fit residues: 20.1209 Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 HIS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 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 266 HIS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 84 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.171434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.147893 restraints weight = 11343.879| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.76 r_work: 0.3703 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.160 Angle : 0.545 7.577 11700 Z= 0.286 Chirality : 0.041 0.135 1359 Planarity : 0.004 0.053 1485 Dihedral : 4.784 44.218 1207 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.96 % Allowed : 28.69 % Favored : 66.35 % 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: -0.38 (0.26), residues: 1103 helix: 1.66 (0.28), residues: 369 sheet: -0.79 (0.32), residues: 287 loop : -1.50 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.021 0.002 TYR R 191 PHE 0.026 0.002 PHE R 324 TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8600) covalent geometry : angle 0.54450 (11694) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.59427 ( 6) hydrogen bonds : bond 0.03418 ( 371) hydrogen bonds : angle 4.37532 ( 1071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.254 Fit side-chains REVERT: R 192 THR cc_start: 0.7971 (m) cc_final: 0.7684 (m) REVERT: R 226 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5563 (tt) REVERT: R 421 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5886 (p90) REVERT: A 271 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7811 (tp) REVERT: B 49 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6957 (mtt-85) REVERT: B 83 ASP cc_start: 0.8109 (t0) cc_final: 0.7701 (t0) REVERT: N 52 SER cc_start: 0.8062 (m) cc_final: 0.7717 (t) outliers start: 42 outliers final: 37 residues processed: 172 average time/residue: 0.0809 time to fit residues: 19.7901 Evaluate side-chains 188 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 HIS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 342 VAL Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 373 LEU Chi-restraints excluded: chain R residue 421 TYR Chi-restraints excluded: chain R residue 429 TYR Chi-restraints excluded: chain R residue 460 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 221 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 266 HIS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain N residue 193 MET Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 13 optimal weight: 0.0770 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.171768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148198 restraints weight = 11323.382| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.76 r_work: 0.3701 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8603 Z= 0.152 Angle : 0.541 7.437 11700 Z= 0.284 Chirality : 0.041 0.144 1359 Planarity : 0.004 0.053 1485 Dihedral : 4.759 43.642 1207 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.08 % Allowed : 28.10 % Favored : 66.82 % 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: -0.36 (0.26), residues: 1103 helix: 1.69 (0.29), residues: 368 sheet: -0.74 (0.32), residues: 283 loop : -1.52 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.021 0.002 TYR R 191 PHE 0.023 0.001 PHE R 324 TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS R 442 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8600) covalent geometry : angle 0.54079 (11694) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.60662 ( 6) hydrogen bonds : bond 0.03371 ( 371) hydrogen bonds : angle 4.35103 ( 1071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2456.18 seconds wall clock time: 42 minutes 46.67 seconds (2566.67 seconds total)