Starting phenix.real_space_refine on Fri Aug 22 20:45:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u02_41776/08_2025/8u02_41776.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u02_41776/08_2025/8u02_41776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u02_41776/08_2025/8u02_41776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u02_41776/08_2025/8u02_41776.map" model { file = "/net/cci-nas-00/data/ceres_data/8u02_41776/08_2025/8u02_41776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u02_41776/08_2025/8u02_41776.cif" } resolution = 3.28 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= -0.000 sd= 0.011 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 59 5.16 5 C 4956 2.51 5 N 1299 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7774 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2136 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2657 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 6, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2544 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 426 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.26 Number of scatterers: 7774 At special positions: 0 Unit cell: (83.904, 101.384, 130.226, 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 59 16.00 O 1460 8.00 N 1299 7.00 C 4956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " 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: 0.70 Conformation dependent library (CDL) restraints added in 476.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 50.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 41 through 61 Processing helix chain 'R' and resid 67 through 87 Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 143 removed outlier: 3.503A pdb=" N TYR R 142 " --> pdb=" O MET R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 169 through 172 removed outlier: 3.600A pdb=" N PHE R 172 " --> pdb=" O PRO R 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 169 through 172' Processing helix chain 'R' and resid 186 through 198 removed outlier: 4.166A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 224 removed outlier: 3.555A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 399 removed outlier: 4.356A pdb=" N ALA R 376 " --> pdb=" O THR R 372 " (cutoff:3.500A) Proline residue: R 388 - end of helix removed outlier: 4.208A pdb=" N ILE R 397 " --> pdb=" O HIS R 393 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 428 removed outlier: 3.521A pdb=" N TYR R 416 " --> pdb=" O THR R 412 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.006A pdb=" N LYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 69 through 92 Processing helix chain 'B' and resid 98 through 113 removed outlier: 4.208A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.697A pdb=" N GLN B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.731A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 229 through 233 removed outlier: 4.028A pdb=" N ASP B 232 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 331 through 352 Processing helix chain 'A' and resid 3 through 24 Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.742A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 192 removed outlier: 6.518A pdb=" N VAL B 34 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE B 200 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU B 36 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N ALA B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 51 removed outlier: 6.902A pdb=" N ILE A 338 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR A 50 " --> pdb=" O LEU A 336 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 336 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 63 removed outlier: 3.913A pdb=" N SER A 74 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 79 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 92 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 81 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.991A pdb=" N GLY A 115 " --> pdb=" O MET A 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS A 103 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA A 113 " --> pdb=" O CYS A 103 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR A 105 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR A 111 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N CYS A 121 " --> pdb=" O GLU A 138 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 138 " --> pdb=" O CYS A 121 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 123 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 134 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 153 removed outlier: 3.727A pdb=" N CYS A 148 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP A 170 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN A 176 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 187 through 192 removed outlier: 3.698A pdb=" N SER A 189 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP A 212 " --> pdb=" O CYS A 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS A 218 " --> pdb=" O ASP A 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 229 through 234 removed outlier: 3.527A pdb=" N ALA A 231 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS A 250 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR A 263 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 252 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.848A pdb=" N SER A 275 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS A 294 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL A 307 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 296 " --> pdb=" O ALA A 305 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1281 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: 1.30 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2510 1.34 - 1.46: 1767 1.46 - 1.58: 3559 1.58 - 1.70: 0 1.70 - 1.83: 85 Bond restraints: 7921 Sorted by residual: bond pdb=" N ILE B 213 " pdb=" CA ILE B 213 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE B 286 " pdb=" CA ILE B 286 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.22e+00 bond pdb=" N TRP B 212 " pdb=" CA TRP B 212 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.35e-02 5.49e+03 8.05e+00 bond pdb=" N THR R 205 " pdb=" CA THR R 205 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.41e+00 bond pdb=" N CYS B 287 " pdb=" CA CYS B 287 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.28e-02 6.10e+03 7.34e+00 ... (remaining 7916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 9806 1.63 - 3.26: 805 3.26 - 4.89: 126 4.89 - 6.52: 19 6.52 - 8.15: 8 Bond angle restraints: 10764 Sorted by residual: angle pdb=" N GLU B 43 " pdb=" CA GLU B 43 " pdb=" C GLU B 43 " ideal model delta sigma weight residual 111.69 103.54 8.15 1.23e+00 6.61e-01 4.40e+01 angle pdb=" N ARG B 179 " pdb=" CA ARG B 179 " pdb=" C ARG B 179 " ideal model delta sigma weight residual 112.24 105.31 6.93 1.28e+00 6.10e-01 2.93e+01 angle pdb=" N ILE R 212 " pdb=" CA ILE R 212 " pdb=" C ILE R 212 " ideal model delta sigma weight residual 110.62 105.51 5.11 1.02e+00 9.61e-01 2.51e+01 angle pdb=" CA LEU B 353 " pdb=" C LEU B 353 " pdb=" O LEU B 353 " ideal model delta sigma weight residual 121.16 115.77 5.39 1.12e+00 7.97e-01 2.32e+01 angle pdb=" N LEU B 353 " pdb=" CA LEU B 353 " pdb=" C LEU B 353 " ideal model delta sigma weight residual 110.28 103.22 7.06 1.48e+00 4.57e-01 2.27e+01 ... (remaining 10759 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 4531 16.95 - 33.89: 124 33.89 - 50.84: 40 50.84 - 67.78: 9 67.78 - 84.73: 6 Dihedral angle restraints: 4710 sinusoidal: 1746 harmonic: 2964 Sorted by residual: dihedral pdb=" CD ARG B 209 " pdb=" NE ARG B 209 " pdb=" CZ ARG B 209 " pdb=" NH1 ARG B 209 " ideal model delta sinusoidal sigma weight residual 0.00 -84.73 84.73 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " pdb=" CZ ARG A 129 " pdb=" NH1 ARG A 129 " ideal model delta sinusoidal sigma weight residual 0.00 40.13 -40.13 1 1.00e+01 1.00e-02 2.26e+01 dihedral pdb=" C ASP A 205 " pdb=" N ASP A 205 " pdb=" CA ASP A 205 " pdb=" CB ASP A 205 " ideal model delta harmonic sigma weight residual -122.60 -113.37 -9.23 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 931 0.055 - 0.110: 257 0.110 - 0.165: 65 0.165 - 0.220: 14 0.220 - 0.274: 2 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA ASP A 205 " pdb=" N ASP A 205 " pdb=" C ASP A 205 " pdb=" CB ASP A 205 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA LEU B 353 " pdb=" N LEU B 353 " pdb=" C LEU B 353 " pdb=" CB LEU B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE R 212 " pdb=" N ILE R 212 " pdb=" C ILE R 212 " pdb=" CB ILE R 212 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1266 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 209 " -0.967 9.50e-02 1.11e+02 4.34e-01 1.22e+02 pdb=" NE ARG B 209 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG B 209 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG B 209 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 209 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 129 " -0.704 9.50e-02 1.11e+02 3.16e-01 6.07e+01 pdb=" NE ARG A 129 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG A 129 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 129 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 129 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 382 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C PHE R 382 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE R 382 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE R 383 " 0.024 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1281 2.76 - 3.29: 8013 3.29 - 3.83: 13215 3.83 - 4.36: 16249 4.36 - 4.90: 26749 Nonbonded interactions: 65507 Sorted by model distance: nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.222 3.040 nonbonded pdb=" OG SER B 126 " pdb=" NH1 ARG B 130 " model vdw 2.258 3.120 nonbonded pdb=" CD1 LEU R 216 " pdb=" OH TYR B 354 " model vdw 2.274 3.460 nonbonded pdb=" O CYS B 255 " pdb=" NZ LYS B 317 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU B 217 " pdb=" NZ LYS A 57 " model vdw 2.279 3.120 ... (remaining 65502 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: 4.920 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.041 7922 Z= 0.307 Angle : 0.977 8.155 10766 Z= 0.649 Chirality : 0.056 0.274 1269 Planarity : 0.016 0.434 1360 Dihedral : 10.236 84.730 2785 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.61 % Allowed : 1.33 % Favored : 98.06 % 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: 0.65 (0.25), residues: 1001 helix: 0.46 (0.21), residues: 465 sheet: 1.39 (0.38), residues: 172 loop : 0.13 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.002 ARG B 209 TYR 0.040 0.003 TYR B 69 PHE 0.027 0.003 PHE A 234 TRP 0.034 0.004 TRP A 63 HIS 0.010 0.002 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 7921) covalent geometry : angle 0.97657 (10764) SS BOND : bond 0.00149 ( 1) SS BOND : angle 2.97066 ( 2) hydrogen bonds : bond 0.15352 ( 438) hydrogen bonds : angle 6.48093 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 218 ASP cc_start: 0.8420 (p0) cc_final: 0.8028 (p0) REVERT: B 263 THR cc_start: 0.8988 (m) cc_final: 0.8754 (p) REVERT: B 307 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8298 (mm110) REVERT: A 14 LEU cc_start: 0.9348 (mt) cc_final: 0.9041 (mt) REVERT: A 59 TYR cc_start: 0.8269 (m-80) cc_final: 0.8019 (m-80) outliers start: 5 outliers final: 1 residues processed: 270 average time/residue: 0.1160 time to fit residues: 40.4268 Evaluate side-chains 163 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 418 ASN B 173 GLN B 196 HIS B 214 HIS B 245 HIS B 307 GLN A 62 HIS C 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072977 restraints weight = 19548.034| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.17 r_work: 0.3049 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7922 Z= 0.193 Angle : 0.691 8.835 10766 Z= 0.365 Chirality : 0.045 0.196 1269 Planarity : 0.004 0.040 1360 Dihedral : 4.723 46.619 1086 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.67 % Allowed : 11.53 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.27), residues: 1001 helix: 1.57 (0.23), residues: 479 sheet: 1.17 (0.38), residues: 181 loop : 0.08 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 218 TYR 0.027 0.002 TYR B 69 PHE 0.032 0.002 PHE A 241 TRP 0.019 0.002 TRP A 169 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 7921) covalent geometry : angle 0.69005 (10764) SS BOND : bond 0.00185 ( 1) SS BOND : angle 2.32205 ( 2) hydrogen bonds : bond 0.04671 ( 438) hydrogen bonds : angle 4.59136 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 131 ASP cc_start: 0.9002 (t70) cc_final: 0.8686 (t70) REVERT: R 369 LYS cc_start: 0.9353 (mttt) cc_final: 0.9044 (mttt) REVERT: R 370 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8461 (ttmt) REVERT: R 373 GLN cc_start: 0.8817 (tt0) cc_final: 0.8481 (pp30) REVERT: R 394 ILE cc_start: 0.8993 (pt) cc_final: 0.8621 (mm) REVERT: B 39 LEU cc_start: 0.8852 (mm) cc_final: 0.8491 (mp) REVERT: B 79 GLN cc_start: 0.7887 (tt0) cc_final: 0.7564 (tm-30) REVERT: B 128 MET cc_start: 0.8915 (mtp) cc_final: 0.8459 (mtp) REVERT: B 249 MET cc_start: 0.9485 (mtm) cc_final: 0.9244 (mmt) REVERT: A 217 MET cc_start: 0.8881 (ppp) cc_final: 0.8484 (ppp) REVERT: A 228 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: A 280 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8781 (tmmt) REVERT: A 317 CYS cc_start: 0.8150 (m) cc_final: 0.7392 (p) REVERT: C 21 MET cc_start: 0.8507 (tmm) cc_final: 0.8243 (tmm) outliers start: 22 outliers final: 9 residues processed: 183 average time/residue: 0.0914 time to fit residues: 23.0515 Evaluate side-chains 153 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 84 optimal weight: 0.0070 chunk 4 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 268 ASN A 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.108963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075742 restraints weight = 19628.708| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 4.36 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7922 Z= 0.127 Angle : 0.604 11.088 10766 Z= 0.316 Chirality : 0.043 0.167 1269 Planarity : 0.004 0.044 1360 Dihedral : 4.331 41.411 1085 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.94 % Allowed : 12.86 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.27), residues: 1001 helix: 1.75 (0.23), residues: 480 sheet: 1.14 (0.37), residues: 185 loop : -0.13 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 219 TYR 0.021 0.001 TYR B 69 PHE 0.024 0.002 PHE A 241 TRP 0.019 0.002 TRP A 169 HIS 0.009 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7921) covalent geometry : angle 0.60379 (10764) SS BOND : bond 0.00005 ( 1) SS BOND : angle 1.67165 ( 2) hydrogen bonds : bond 0.04036 ( 438) hydrogen bonds : angle 4.27716 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 131 ASP cc_start: 0.8674 (t70) cc_final: 0.8379 (t70) REVERT: R 164 PHE cc_start: 0.8788 (t80) cc_final: 0.8550 (t80) REVERT: R 369 LYS cc_start: 0.9311 (mttt) cc_final: 0.8928 (pttp) REVERT: R 370 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8314 (ttmt) REVERT: R 373 GLN cc_start: 0.8709 (tt0) cc_final: 0.8288 (pp30) REVERT: R 382 PHE cc_start: 0.7684 (t80) cc_final: 0.7435 (t80) REVERT: B 20 GLU cc_start: 0.9334 (tp30) cc_final: 0.8908 (tp30) REVERT: B 53 MET cc_start: 0.9053 (mtm) cc_final: 0.8829 (mtm) REVERT: B 88 MET cc_start: 0.5252 (mmm) cc_final: 0.5013 (tpt) REVERT: B 128 MET cc_start: 0.8872 (mtp) cc_final: 0.8533 (mtp) REVERT: B 217 GLU cc_start: 0.8755 (pt0) cc_final: 0.8518 (pt0) REVERT: B 249 MET cc_start: 0.9248 (mtm) cc_final: 0.8973 (mmt) REVERT: B 278 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8324 (ttmt) REVERT: B 308 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8176 (m-10) REVERT: A 13 GLN cc_start: 0.9466 (pp30) cc_final: 0.9070 (pp30) REVERT: A 61 MET cc_start: 0.8391 (tmm) cc_final: 0.8154 (tmm) REVERT: A 172 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8466 (mp0) REVERT: A 217 MET cc_start: 0.8416 (ppp) cc_final: 0.7904 (ppp) REVERT: A 280 LYS cc_start: 0.8853 (tmtt) cc_final: 0.8418 (tmtt) REVERT: C 38 MET cc_start: 0.8438 (mtp) cc_final: 0.8009 (ptp) REVERT: C 42 GLU cc_start: 0.9117 (pp20) cc_final: 0.8789 (mm-30) outliers start: 16 outliers final: 10 residues processed: 175 average time/residue: 0.0919 time to fit residues: 21.9602 Evaluate side-chains 153 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain A residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 13 GLN A 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.105721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072625 restraints weight = 19886.151| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.31 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7922 Z= 0.165 Angle : 0.608 10.197 10766 Z= 0.316 Chirality : 0.043 0.162 1269 Planarity : 0.004 0.049 1360 Dihedral : 4.404 46.109 1085 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.16 % Allowed : 12.74 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.27), residues: 1001 helix: 1.95 (0.24), residues: 475 sheet: 1.03 (0.37), residues: 183 loop : -0.23 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 256 TYR 0.020 0.001 TYR A 85 PHE 0.023 0.002 PHE A 241 TRP 0.015 0.002 TRP A 82 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7921) covalent geometry : angle 0.60791 (10764) SS BOND : bond 0.00202 ( 1) SS BOND : angle 1.57513 ( 2) hydrogen bonds : bond 0.03923 ( 438) hydrogen bonds : angle 4.25490 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.9271 (mt) cc_final: 0.8908 (tp) REVERT: R 82 LEU cc_start: 0.8826 (mt) cc_final: 0.8587 (mp) REVERT: R 131 ASP cc_start: 0.8763 (t70) cc_final: 0.8491 (t70) REVERT: R 164 PHE cc_start: 0.8855 (t80) cc_final: 0.8630 (t80) REVERT: R 174 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6257 (pp) REVERT: R 369 LYS cc_start: 0.9342 (mttt) cc_final: 0.8941 (pttp) REVERT: R 370 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8340 (ttmt) REVERT: R 373 GLN cc_start: 0.8792 (tt0) cc_final: 0.8471 (pp30) REVERT: B 53 MET cc_start: 0.9021 (mtm) cc_final: 0.8767 (mtm) REVERT: B 217 GLU cc_start: 0.8852 (pt0) cc_final: 0.8650 (pt0) REVERT: B 249 MET cc_start: 0.9241 (mtm) cc_final: 0.9002 (mmt) REVERT: B 307 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8304 (tp-100) REVERT: A 13 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9198 (pp30) REVERT: A 61 MET cc_start: 0.8501 (tmm) cc_final: 0.8157 (tmm) REVERT: A 246 ASP cc_start: 0.8479 (m-30) cc_final: 0.8066 (m-30) REVERT: A 280 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8540 (tmtt) outliers start: 26 outliers final: 14 residues processed: 165 average time/residue: 0.0931 time to fit residues: 20.9709 Evaluate side-chains 150 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.104787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071447 restraints weight = 19956.189| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.35 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7922 Z= 0.177 Angle : 0.628 11.258 10766 Z= 0.320 Chirality : 0.043 0.156 1269 Planarity : 0.004 0.049 1360 Dihedral : 4.488 51.016 1085 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.40 % Allowed : 14.20 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.27), residues: 1001 helix: 1.86 (0.24), residues: 481 sheet: 0.71 (0.36), residues: 188 loop : -0.42 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.022 0.001 TYR A 85 PHE 0.021 0.002 PHE A 241 TRP 0.030 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 7921) covalent geometry : angle 0.62762 (10764) SS BOND : bond 0.00197 ( 1) SS BOND : angle 1.61761 ( 2) hydrogen bonds : bond 0.03962 ( 438) hydrogen bonds : angle 4.26250 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 88 MET cc_start: 0.9165 (mmt) cc_final: 0.8932 (mmm) REVERT: R 90 TRP cc_start: 0.8250 (m100) cc_final: 0.8012 (m100) REVERT: R 131 ASP cc_start: 0.8839 (t70) cc_final: 0.8575 (t70) REVERT: R 164 PHE cc_start: 0.8851 (t80) cc_final: 0.8628 (t80) REVERT: R 174 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6315 (pp) REVERT: R 369 LYS cc_start: 0.9318 (mttt) cc_final: 0.8916 (pttp) REVERT: R 373 GLN cc_start: 0.8919 (tt0) cc_final: 0.8556 (pp30) REVERT: B 249 MET cc_start: 0.9240 (mtm) cc_final: 0.9009 (mmt) REVERT: A 13 GLN cc_start: 0.9647 (pp30) cc_final: 0.9438 (pp30) REVERT: A 61 MET cc_start: 0.8523 (tmm) cc_final: 0.8154 (tmm) REVERT: A 246 ASP cc_start: 0.8483 (m-30) cc_final: 0.8235 (m-30) REVERT: A 280 LYS cc_start: 0.9010 (tmtt) cc_final: 0.8501 (tmmt) outliers start: 28 outliers final: 21 residues processed: 160 average time/residue: 0.0914 time to fit residues: 20.1273 Evaluate side-chains 152 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 13 GLN A 32 GLN A 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.104580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.071525 restraints weight = 19940.554| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 4.35 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7922 Z= 0.174 Angle : 0.625 10.540 10766 Z= 0.318 Chirality : 0.042 0.161 1269 Planarity : 0.004 0.049 1360 Dihedral : 4.533 57.384 1085 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.52 % Allowed : 15.53 % Favored : 80.95 % 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: 1.27 (0.27), residues: 1001 helix: 1.86 (0.24), residues: 481 sheet: 0.65 (0.36), residues: 186 loop : -0.49 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.027 0.001 TYR B 69 PHE 0.021 0.002 PHE A 241 TRP 0.025 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7921) covalent geometry : angle 0.62476 (10764) SS BOND : bond 0.00259 ( 1) SS BOND : angle 1.41880 ( 2) hydrogen bonds : bond 0.03872 ( 438) hydrogen bonds : angle 4.32691 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.7698 (mp0) cc_final: 0.7331 (mp0) REVERT: R 90 TRP cc_start: 0.8247 (m100) cc_final: 0.7919 (m100) REVERT: R 131 ASP cc_start: 0.8842 (t70) cc_final: 0.8532 (t0) REVERT: R 174 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6438 (pp) REVERT: R 369 LYS cc_start: 0.9342 (mttt) cc_final: 0.8915 (pttp) REVERT: R 373 GLN cc_start: 0.8912 (tt0) cc_final: 0.8537 (pp30) REVERT: B 249 MET cc_start: 0.9236 (mtm) cc_final: 0.9033 (mmt) REVERT: B 323 MET cc_start: 0.8457 (mtp) cc_final: 0.8082 (mmm) REVERT: A 61 MET cc_start: 0.8520 (tmm) cc_final: 0.7956 (tmm) REVERT: A 246 ASP cc_start: 0.8585 (m-30) cc_final: 0.8382 (m-30) REVERT: A 280 LYS cc_start: 0.9033 (tmtt) cc_final: 0.8519 (tmmt) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 0.0910 time to fit residues: 19.4605 Evaluate side-chains 149 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS A 75 GLN A 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.106017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.073096 restraints weight = 19960.147| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 4.42 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7922 Z= 0.131 Angle : 0.639 13.788 10766 Z= 0.312 Chirality : 0.042 0.193 1269 Planarity : 0.003 0.048 1360 Dihedral : 4.377 52.548 1085 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.64 % Allowed : 17.11 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.27), residues: 1001 helix: 1.86 (0.24), residues: 481 sheet: 0.78 (0.37), residues: 183 loop : -0.51 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.022 0.001 TYR B 69 PHE 0.019 0.001 PHE A 241 TRP 0.021 0.002 TRP R 90 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7921) covalent geometry : angle 0.63924 (10764) SS BOND : bond 0.00069 ( 1) SS BOND : angle 1.22088 ( 2) hydrogen bonds : bond 0.03576 ( 438) hydrogen bonds : angle 4.24276 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.9264 (mt) cc_final: 0.8974 (tp) REVERT: R 62 GLU cc_start: 0.7602 (mp0) cc_final: 0.7262 (mp0) REVERT: R 88 MET cc_start: 0.9209 (mmt) cc_final: 0.8980 (mmm) REVERT: R 131 ASP cc_start: 0.8779 (t70) cc_final: 0.8560 (t0) REVERT: R 174 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6573 (pp) REVERT: R 369 LYS cc_start: 0.9320 (mttt) cc_final: 0.8876 (pttp) REVERT: R 373 GLN cc_start: 0.8842 (tt0) cc_final: 0.8467 (pp30) REVERT: B 128 MET cc_start: 0.8619 (mmt) cc_final: 0.8371 (mmp) REVERT: B 249 MET cc_start: 0.9266 (mtm) cc_final: 0.9028 (mmt) REVERT: B 278 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8205 (ttmt) REVERT: B 323 MET cc_start: 0.8464 (mtp) cc_final: 0.8094 (mmm) REVERT: A 13 GLN cc_start: 0.9542 (tm-30) cc_final: 0.9236 (pp30) REVERT: A 61 MET cc_start: 0.8524 (tmm) cc_final: 0.8109 (tmm) REVERT: A 172 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8688 (tm-30) REVERT: A 246 ASP cc_start: 0.8597 (m-30) cc_final: 0.8337 (m-30) REVERT: A 280 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8397 (tmmt) REVERT: C 48 ASP cc_start: 0.8505 (t70) cc_final: 0.8036 (t70) outliers start: 30 outliers final: 20 residues processed: 174 average time/residue: 0.1046 time to fit residues: 23.6593 Evaluate side-chains 161 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS A 44 GLN A 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.108056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075470 restraints weight = 20107.731| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.03 r_work: 0.3147 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7922 Z= 0.134 Angle : 0.638 12.539 10766 Z= 0.315 Chirality : 0.042 0.194 1269 Planarity : 0.004 0.048 1360 Dihedral : 4.334 52.907 1085 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.16 % Allowed : 17.96 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.27), residues: 1001 helix: 1.82 (0.24), residues: 481 sheet: 0.73 (0.37), residues: 175 loop : -0.52 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.020 0.001 TYR B 69 PHE 0.019 0.001 PHE A 241 TRP 0.018 0.001 TRP R 90 HIS 0.003 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 7921) covalent geometry : angle 0.63788 (10764) SS BOND : bond 0.00168 ( 1) SS BOND : angle 1.12915 ( 2) hydrogen bonds : bond 0.03607 ( 438) hydrogen bonds : angle 4.24803 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.7884 (mp0) cc_final: 0.7509 (mp0) REVERT: R 82 LEU cc_start: 0.8902 (mt) cc_final: 0.8686 (mp) REVERT: R 174 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6954 (pp) REVERT: R 369 LYS cc_start: 0.9346 (mttt) cc_final: 0.8806 (ptmt) REVERT: B 20 GLU cc_start: 0.9337 (tp30) cc_final: 0.9131 (tp30) REVERT: B 109 ASP cc_start: 0.9537 (m-30) cc_final: 0.9026 (t0) REVERT: B 128 MET cc_start: 0.8765 (mmt) cc_final: 0.8494 (mmp) REVERT: B 249 MET cc_start: 0.9453 (mtm) cc_final: 0.9232 (mmt) REVERT: B 278 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8324 (ttmt) REVERT: B 322 HIS cc_start: 0.8813 (t-90) cc_final: 0.8462 (t-90) REVERT: B 323 MET cc_start: 0.8681 (mtp) cc_final: 0.8357 (mmm) REVERT: A 13 GLN cc_start: 0.9510 (tm-30) cc_final: 0.9198 (pp30) REVERT: A 61 MET cc_start: 0.8958 (tmm) cc_final: 0.8542 (tmm) REVERT: A 127 LYS cc_start: 0.9270 (mmmt) cc_final: 0.8967 (mmmt) REVERT: A 172 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8946 (tm-30) REVERT: A 246 ASP cc_start: 0.8850 (m-30) cc_final: 0.8600 (m-30) REVERT: A 280 LYS cc_start: 0.9170 (tmtt) cc_final: 0.8675 (tmmt) REVERT: C 48 ASP cc_start: 0.8737 (t70) cc_final: 0.7851 (t0) outliers start: 26 outliers final: 21 residues processed: 165 average time/residue: 0.1126 time to fit residues: 24.3926 Evaluate side-chains 170 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.110555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077781 restraints weight = 20096.720| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 4.06 r_work: 0.3210 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7922 Z= 0.124 Angle : 0.658 13.563 10766 Z= 0.320 Chirality : 0.042 0.190 1269 Planarity : 0.004 0.047 1360 Dihedral : 4.293 52.308 1085 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.43 % Allowed : 19.17 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.27), residues: 1001 helix: 1.87 (0.24), residues: 475 sheet: 0.75 (0.37), residues: 174 loop : -0.56 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.019 0.001 TYR B 69 PHE 0.018 0.001 PHE A 241 TRP 0.016 0.001 TRP A 169 HIS 0.003 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7921) covalent geometry : angle 0.65824 (10764) SS BOND : bond 0.00107 ( 1) SS BOND : angle 1.03000 ( 2) hydrogen bonds : bond 0.03490 ( 438) hydrogen bonds : angle 4.22267 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 62 GLU cc_start: 0.7895 (mp0) cc_final: 0.7048 (mp0) REVERT: R 174 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7049 (pp) REVERT: R 369 LYS cc_start: 0.9296 (mttt) cc_final: 0.8815 (ptmt) REVERT: B 109 ASP cc_start: 0.9549 (m-30) cc_final: 0.9149 (t0) REVERT: B 128 MET cc_start: 0.8792 (mmt) cc_final: 0.8541 (mmp) REVERT: B 249 MET cc_start: 0.9428 (mtm) cc_final: 0.9217 (mmt) REVERT: B 278 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8419 (ttmt) REVERT: B 322 HIS cc_start: 0.8813 (t-90) cc_final: 0.8494 (t-90) REVERT: B 323 MET cc_start: 0.8681 (mtp) cc_final: 0.8377 (mmm) REVERT: A 13 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9140 (pp30) REVERT: A 61 MET cc_start: 0.8888 (tmm) cc_final: 0.8482 (tmm) REVERT: A 127 LYS cc_start: 0.9280 (mmmt) cc_final: 0.9009 (mmmt) REVERT: A 172 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8980 (tm-30) REVERT: A 246 ASP cc_start: 0.8839 (m-30) cc_final: 0.8586 (m-30) REVERT: A 280 LYS cc_start: 0.9200 (tmtt) cc_final: 0.8748 (tmmt) REVERT: C 48 ASP cc_start: 0.8675 (t70) cc_final: 0.8163 (t70) outliers start: 20 outliers final: 16 residues processed: 161 average time/residue: 0.1146 time to fit residues: 24.0215 Evaluate side-chains 154 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Chi-restraints excluded: chain C residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.110074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.077350 restraints weight = 19978.486| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 4.05 r_work: 0.3204 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7922 Z= 0.138 Angle : 0.681 14.377 10766 Z= 0.334 Chirality : 0.043 0.185 1269 Planarity : 0.004 0.064 1360 Dihedral : 4.354 54.311 1085 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.55 % Allowed : 19.90 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.27), residues: 1001 helix: 1.77 (0.24), residues: 475 sheet: 0.57 (0.37), residues: 177 loop : -0.48 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 222 TYR 0.019 0.001 TYR B 69 PHE 0.018 0.001 PHE A 241 TRP 0.017 0.001 TRP A 82 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 7921) covalent geometry : angle 0.68074 (10764) SS BOND : bond 0.00171 ( 1) SS BOND : angle 1.03087 ( 2) hydrogen bonds : bond 0.03500 ( 438) hydrogen bonds : angle 4.28822 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 149 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8494 (mmmm) REVERT: R 174 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7201 (pp) REVERT: R 192 TYR cc_start: 0.8536 (m-10) cc_final: 0.8262 (m-80) REVERT: R 369 LYS cc_start: 0.9292 (mttt) cc_final: 0.8807 (ptmt) REVERT: B 278 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8411 (ttmt) REVERT: B 322 HIS cc_start: 0.8817 (t-90) cc_final: 0.8496 (t-90) REVERT: B 323 MET cc_start: 0.8712 (mtp) cc_final: 0.7993 (mmm) REVERT: A 13 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9130 (pp30) REVERT: A 61 MET cc_start: 0.8906 (tmm) cc_final: 0.8483 (tmm) REVERT: A 127 LYS cc_start: 0.9289 (mmmt) cc_final: 0.9018 (mmmt) REVERT: A 172 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8965 (tm-30) REVERT: A 246 ASP cc_start: 0.8828 (m-30) cc_final: 0.8568 (m-30) REVERT: A 280 LYS cc_start: 0.9201 (tmtt) cc_final: 0.8744 (tmtt) REVERT: C 26 ASP cc_start: 0.9131 (m-30) cc_final: 0.8774 (t0) REVERT: C 48 ASP cc_start: 0.8704 (t70) cc_final: 0.8033 (t70) outliers start: 21 outliers final: 18 residues processed: 158 average time/residue: 0.0923 time to fit residues: 20.0138 Evaluate side-chains 160 residues out of total 877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 108 ASP Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 407 LEU Chi-restraints excluded: chain R residue 418 ASN Chi-restraints excluded: chain R residue 421 VAL Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 HIS A 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075948 restraints weight = 19832.946| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.05 r_work: 0.3159 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7922 Z= 0.147 Angle : 0.723 14.362 10766 Z= 0.353 Chirality : 0.044 0.177 1269 Planarity : 0.004 0.048 1360 Dihedral : 4.420 57.631 1085 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.31 % Allowed : 20.51 % Favored : 77.18 % 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: 1.12 (0.27), residues: 1001 helix: 1.68 (0.24), residues: 479 sheet: 0.56 (0.37), residues: 176 loop : -0.43 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 113 TYR 0.018 0.001 TYR B 69 PHE 0.018 0.001 PHE A 241 TRP 0.019 0.002 TRP B 132 HIS 0.004 0.001 HIS R 393 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7921) covalent geometry : angle 0.72339 (10764) SS BOND : bond 0.00194 ( 1) SS BOND : angle 1.04746 ( 2) hydrogen bonds : bond 0.03641 ( 438) hydrogen bonds : angle 4.36125 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.75 seconds wall clock time: 40 minutes 38.95 seconds (2438.95 seconds total)