Starting phenix.real_space_refine on Wed Sep 17 12:18:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqe_60384/09_2025/8zqe_60384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqe_60384/09_2025/8zqe_60384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zqe_60384/09_2025/8zqe_60384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqe_60384/09_2025/8zqe_60384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zqe_60384/09_2025/8zqe_60384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqe_60384/09_2025/8zqe_60384.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5602 2.51 5 N 1490 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8767 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2192 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 75 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 2, 'TRANS': 7} Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8767 At special positions: 0 Unit cell: (86.528, 117.312, 125.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1611 8.00 N 1490 7.00 C 5602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " 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: 0.73 Conformation dependent library (CDL) restraints added in 448.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.9% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.576A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.590A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.724A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.844A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 61 through 65 removed outlier: 3.582A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.965A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.655A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 61 removed outlier: 3.633A pdb=" N ALA R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 3.780A pdb=" N ILE R 70 " --> pdb=" O ARG R 66 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N THR R 85 " --> pdb=" O ILE R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.985A pdb=" N TRP R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.590A pdb=" N SER R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 172 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 189 through 202 Processing helix chain 'R' and resid 204 through 229 removed outlier: 3.566A pdb=" N THR R 213 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER R 229 " --> pdb=" O HIS R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 270 removed outlier: 3.962A pdb=" N SER R 239 " --> pdb=" O LYS R 235 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 278 through 288 Processing helix chain 'R' and resid 289 through 291 No H-bonds generated for 'chain 'R' and resid 289 through 291' Processing helix chain 'R' and resid 292 through 305 removed outlier: 3.623A pdb=" N ASN R 298 " --> pdb=" O ASN R 294 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.849A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.229A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.719A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.385A 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: 6.621A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.621A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.545A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.639A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.716A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.418A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.754A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 135 removed outlier: 3.520A pdb=" N TYR S 215 " --> pdb=" O THR S 231 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 175 through 177 442 hydrogen bonds defined for protein. 1242 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: 1.32 Time building geometry restraints manager: 0.98 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: 2213 1.33 - 1.45: 1854 1.45 - 1.58: 4797 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 8953 Sorted by residual: bond pdb=" N GLN B 175 " pdb=" CA GLN B 175 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.44e+01 bond pdb=" N VAL L 74 " pdb=" CA VAL L 74 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.10e-03 1.21e+04 1.34e+01 bond pdb=" N TRP R 89 " pdb=" CA TRP R 89 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.28e-02 6.10e+03 1.13e+01 bond pdb=" N VAL L 73 " pdb=" CA VAL L 73 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" N ILE A 344 " pdb=" CA ILE A 344 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.31e+00 ... (remaining 8948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 11617 1.61 - 3.22: 422 3.22 - 4.83: 72 4.83 - 6.44: 13 6.44 - 8.05: 6 Bond angle restraints: 12130 Sorted by residual: angle pdb=" C SER R 229 " pdb=" CA SER R 229 " pdb=" CB SER R 229 " ideal model delta sigma weight residual 116.63 110.91 5.72 1.16e+00 7.43e-01 2.43e+01 angle pdb=" N LEU R 36 " pdb=" CA LEU R 36 " pdb=" C LEU R 36 " ideal model delta sigma weight residual 113.25 107.44 5.81 1.30e+00 5.92e-01 1.99e+01 angle pdb=" N PHE R 82 " pdb=" CA PHE R 82 " pdb=" C PHE R 82 " ideal model delta sigma weight residual 111.36 106.96 4.40 1.09e+00 8.42e-01 1.63e+01 angle pdb=" N SER R 229 " pdb=" CA SER R 229 " pdb=" C SER R 229 " ideal model delta sigma weight residual 108.08 114.70 -6.62 1.69e+00 3.50e-01 1.53e+01 angle pdb=" N PHE A 334 " pdb=" CA PHE A 334 " pdb=" C PHE A 334 " ideal model delta sigma weight residual 111.07 107.04 4.03 1.07e+00 8.73e-01 1.42e+01 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4822 17.86 - 35.72: 401 35.72 - 53.58: 62 53.58 - 71.44: 12 71.44 - 89.30: 8 Dihedral angle restraints: 5305 sinusoidal: 2029 harmonic: 3276 Sorted by residual: dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual -180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 58.75 34.25 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1094 0.054 - 0.107: 232 0.107 - 0.161: 48 0.161 - 0.214: 11 0.214 - 0.268: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CA ILE R 309 " pdb=" N ILE R 309 " pdb=" C ILE R 309 " pdb=" CB ILE R 309 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE R 279 " pdb=" N ILE R 279 " pdb=" C ILE R 279 " pdb=" CB ILE R 279 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA VAL B 307 " pdb=" N VAL B 307 " pdb=" C VAL B 307 " pdb=" CB VAL B 307 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 1383 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 306 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ASP R 306 " -0.060 2.00e-02 2.50e+03 pdb=" O ASP R 306 " 0.023 2.00e-02 2.50e+03 pdb=" N SER R 307 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 166 " 0.052 5.00e-02 4.00e+02 7.78e-02 9.68e+00 pdb=" N PRO R 167 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 167 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 167 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 89 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C TRP R 89 " 0.036 2.00e-02 2.50e+03 pdb=" O TRP R 89 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL R 90 " -0.012 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 334 2.72 - 3.26: 9201 3.26 - 3.81: 14919 3.81 - 4.35: 18338 4.35 - 4.90: 31491 Nonbonded interactions: 74283 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.169 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU R 173 " pdb=" NZ LYS R 186 " model vdw 2.254 3.120 nonbonded pdb=" OG SER S 52 " pdb=" O SER S 55 " model vdw 2.266 3.040 ... (remaining 74278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 0.045 8956 Z= 0.274 Angle : 0.714 8.053 12136 Z= 0.453 Chirality : 0.049 0.268 1386 Planarity : 0.005 0.078 1524 Dihedral : 13.699 89.299 3180 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.21 % Allowed : 0.85 % Favored : 98.94 % 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: -0.15 (0.26), residues: 1111 helix: 0.89 (0.26), residues: 391 sheet: -0.11 (0.33), residues: 270 loop : -0.89 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 190 TYR 0.020 0.002 TYR S 223 PHE 0.014 0.001 PHE A 334 TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8953) covalent geometry : angle 0.71414 (12130) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.89498 ( 6) hydrogen bonds : bond 0.18796 ( 437) hydrogen bonds : angle 7.60646 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7853 (mtmt) REVERT: A 243 MET cc_start: 0.7966 (tpp) cc_final: 0.7049 (tpp) REVERT: A 249 LEU cc_start: 0.8387 (tp) cc_final: 0.8088 (tp) REVERT: A 252 SER cc_start: 0.8467 (t) cc_final: 0.7858 (p) REVERT: A 315 ASP cc_start: 0.7213 (p0) cc_final: 0.6969 (p0) REVERT: B 8 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7807 (ptp-110) REVERT: B 33 ILE cc_start: 0.8317 (pt) cc_final: 0.7994 (mt) REVERT: B 189 SER cc_start: 0.8297 (t) cc_final: 0.7991 (p) REVERT: B 210 LEU cc_start: 0.8122 (tp) cc_final: 0.7882 (tt) REVERT: B 260 GLU cc_start: 0.7136 (pt0) cc_final: 0.6907 (pt0) REVERT: B 261 LEU cc_start: 0.8129 (mt) cc_final: 0.7878 (mm) REVERT: B 262 MET cc_start: 0.7343 (mmt) cc_final: 0.7068 (mmm) REVERT: B 263 THR cc_start: 0.8074 (m) cc_final: 0.7777 (t) REVERT: C 20 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8081 (ttpt) REVERT: S 7 SER cc_start: 0.8340 (t) cc_final: 0.8096 (p) REVERT: S 63 THR cc_start: 0.7866 (t) cc_final: 0.7512 (m) REVERT: S 71 SER cc_start: 0.8281 (p) cc_final: 0.7903 (t) REVERT: S 90 ASP cc_start: 0.7981 (m-30) cc_final: 0.7648 (m-30) REVERT: S 116 THR cc_start: 0.8734 (t) cc_final: 0.8495 (m) REVERT: S 160 THR cc_start: 0.7899 (m) cc_final: 0.7630 (t) REVERT: S 218 MET cc_start: 0.7742 (ttp) cc_final: 0.7539 (ttp) REVERT: R 55 MET cc_start: 0.6273 (mtm) cc_final: 0.5883 (mtm) REVERT: R 124 LEU cc_start: 0.7036 (tp) cc_final: 0.6389 (mt) REVERT: R 200 LEU cc_start: 0.7357 (tp) cc_final: 0.7145 (tt) REVERT: R 300 PHE cc_start: 0.6486 (m-80) cc_final: 0.6240 (m-10) outliers start: 2 outliers final: 2 residues processed: 280 average time/residue: 0.4761 time to fit residues: 143.0799 Evaluate side-chains 236 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 234 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 110 ASN B 155 ASN B 311 HIS B 340 ASN S 130 GLN S 167 GLN S 182 ASN R 233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.144314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121066 restraints weight = 13255.474| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.14 r_work: 0.3504 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 8956 Z= 0.332 Angle : 0.743 9.387 12136 Z= 0.385 Chirality : 0.049 0.211 1386 Planarity : 0.005 0.064 1524 Dihedral : 5.024 24.692 1219 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.86 % Allowed : 13.32 % Favored : 81.82 % 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: -0.20 (0.26), residues: 1111 helix: 1.02 (0.26), residues: 393 sheet: -0.17 (0.31), residues: 290 loop : -1.10 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.027 0.002 TYR S 178 PHE 0.024 0.002 PHE S 68 TRP 0.021 0.003 TRP B 211 HIS 0.008 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00723 ( 8953) covalent geometry : angle 0.74212 (12130) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.32368 ( 6) hydrogen bonds : bond 0.04951 ( 437) hydrogen bonds : angle 5.40543 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 281 time to evaluate : 0.308 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: A 33 GLU cc_start: 0.8265 (pt0) cc_final: 0.7994 (pt0) REVERT: A 190 THR cc_start: 0.8558 (t) cc_final: 0.8329 (m) REVERT: A 197 LYS cc_start: 0.8252 (mttm) cc_final: 0.7702 (mtpp) REVERT: A 243 MET cc_start: 0.8572 (tpp) cc_final: 0.7851 (tpp) REVERT: A 249 LEU cc_start: 0.8617 (tp) cc_final: 0.8283 (tp) REVERT: A 252 SER cc_start: 0.8763 (t) cc_final: 0.8366 (p) REVERT: A 271 LYS cc_start: 0.8537 (pttt) cc_final: 0.7903 (pttm) REVERT: A 310 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 17 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: B 22 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7170 (mtt-85) REVERT: B 96 ARG cc_start: 0.7771 (mpt90) cc_final: 0.7468 (mpt180) REVERT: B 137 ARG cc_start: 0.7732 (mmm160) cc_final: 0.7358 (mmm160) REVERT: B 155 ASN cc_start: 0.8241 (t0) cc_final: 0.7552 (t0) REVERT: B 173 THR cc_start: 0.8465 (p) cc_final: 0.8163 (p) REVERT: B 175 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: B 214 ARG cc_start: 0.8658 (mmt90) cc_final: 0.8440 (mmt90) REVERT: B 221 THR cc_start: 0.8508 (t) cc_final: 0.8234 (m) REVERT: B 261 LEU cc_start: 0.8521 (mt) cc_final: 0.8292 (mm) REVERT: B 262 MET cc_start: 0.8178 (mmt) cc_final: 0.7950 (mmm) REVERT: B 323 ASP cc_start: 0.7956 (p0) cc_final: 0.7708 (p0) REVERT: C 20 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8366 (ttpt) REVERT: C 21 MET cc_start: 0.7833 (ptm) cc_final: 0.7449 (ptm) REVERT: S 58 ILE cc_start: 0.8861 (mm) cc_final: 0.8616 (OUTLIER) REVERT: S 63 THR cc_start: 0.8637 (t) cc_final: 0.8371 (m) REVERT: S 79 LEU cc_start: 0.8013 (tm) cc_final: 0.7783 (tp) REVERT: S 93 MET cc_start: 0.8122 (ttt) cc_final: 0.7887 (ttp) REVERT: S 95 TYR cc_start: 0.8248 (m-80) cc_final: 0.7927 (m-80) REVERT: S 156 SER cc_start: 0.8518 (m) cc_final: 0.8307 (p) REVERT: S 163 TYR cc_start: 0.8410 (m-80) cc_final: 0.8189 (m-80) REVERT: S 180 MET cc_start: 0.6825 (tmm) cc_final: 0.6570 (tmm) REVERT: S 205 SER cc_start: 0.8487 (t) cc_final: 0.8135 (t) REVERT: S 216 TYR cc_start: 0.8602 (m-80) cc_final: 0.8362 (m-80) REVERT: R 55 MET cc_start: 0.7350 (mtm) cc_final: 0.6744 (mtm) REVERT: R 124 LEU cc_start: 0.7440 (tp) cc_final: 0.7077 (mt) REVERT: R 285 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: R 300 PHE cc_start: 0.7399 (m-80) cc_final: 0.7122 (m-10) REVERT: R 301 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8119 (mp) outliers start: 46 outliers final: 14 residues processed: 295 average time/residue: 0.4485 time to fit residues: 142.4366 Evaluate side-chains 293 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 241 LYS Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 75 GLN B 176 GLN B 183 HIS B 230 ASN S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.145755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122853 restraints weight = 13267.148| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.15 r_work: 0.3529 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8956 Z= 0.155 Angle : 0.610 8.749 12136 Z= 0.311 Chirality : 0.044 0.174 1386 Planarity : 0.005 0.058 1524 Dihedral : 4.587 27.944 1216 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.44 % Allowed : 18.39 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1111 helix: 1.13 (0.26), residues: 393 sheet: -0.30 (0.31), residues: 289 loop : -0.84 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 168 TYR 0.037 0.002 TYR S 59 PHE 0.019 0.002 PHE R 204 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8953) covalent geometry : angle 0.60986 (12130) SS BOND : bond 0.00237 ( 3) SS BOND : angle 0.88659 ( 6) hydrogen bonds : bond 0.04083 ( 437) hydrogen bonds : angle 5.04729 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 270 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8222 (pt0) cc_final: 0.7963 (pt0) REVERT: A 190 THR cc_start: 0.8522 (t) cc_final: 0.8295 (m) REVERT: A 197 LYS cc_start: 0.8212 (mttm) cc_final: 0.7648 (mtpp) REVERT: A 243 MET cc_start: 0.8634 (tpp) cc_final: 0.7965 (tpp) REVERT: A 249 LEU cc_start: 0.8576 (tp) cc_final: 0.8245 (tp) REVERT: A 252 SER cc_start: 0.8728 (t) cc_final: 0.8370 (p) REVERT: A 271 LYS cc_start: 0.8539 (pttt) cc_final: 0.7915 (pttm) REVERT: A 330 LYS cc_start: 0.8094 (mppt) cc_final: 0.7769 (mppt) REVERT: B 8 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7957 (ptp-110) REVERT: B 17 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: B 22 ARG cc_start: 0.7405 (mtt180) cc_final: 0.7193 (mtt-85) REVERT: B 96 ARG cc_start: 0.7815 (mpt90) cc_final: 0.7538 (mpt180) REVERT: B 137 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7251 (mmm160) REVERT: B 175 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: B 214 ARG cc_start: 0.8647 (mmt90) cc_final: 0.8428 (mmt90) REVERT: B 221 THR cc_start: 0.8468 (t) cc_final: 0.8168 (m) REVERT: B 251 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7163 (mtm-85) REVERT: B 253 PHE cc_start: 0.8761 (m-80) cc_final: 0.8484 (m-80) REVERT: B 261 LEU cc_start: 0.8568 (mt) cc_final: 0.8316 (mm) REVERT: B 263 THR cc_start: 0.8560 (m) cc_final: 0.8275 (t) REVERT: C 20 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8277 (ttpt) REVERT: C 21 MET cc_start: 0.7812 (ptm) cc_final: 0.7502 (ptm) REVERT: S 57 THR cc_start: 0.8070 (m) cc_final: 0.7778 (p) REVERT: S 63 THR cc_start: 0.8539 (t) cc_final: 0.8234 (m) REVERT: S 79 LEU cc_start: 0.8020 (tm) cc_final: 0.7773 (tp) REVERT: S 180 MET cc_start: 0.6340 (tmm) cc_final: 0.6104 (tmm) REVERT: S 190 ARG cc_start: 0.7691 (mtm-85) cc_final: 0.7234 (ptt-90) REVERT: S 205 SER cc_start: 0.8399 (t) cc_final: 0.8038 (t) REVERT: R 55 MET cc_start: 0.7325 (mtm) cc_final: 0.6712 (mtm) REVERT: R 71 PHE cc_start: 0.7623 (m-10) cc_final: 0.7067 (m-10) REVERT: R 117 MET cc_start: 0.7623 (tmm) cc_final: 0.7392 (tmm) REVERT: R 124 LEU cc_start: 0.7435 (tp) cc_final: 0.7171 (mt) REVERT: R 300 PHE cc_start: 0.7440 (m-80) cc_final: 0.7138 (m-10) REVERT: R 301 ILE cc_start: 0.8234 (mm) cc_final: 0.8026 (mp) outliers start: 42 outliers final: 19 residues processed: 278 average time/residue: 0.5063 time to fit residues: 150.9716 Evaluate side-chains 283 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 261 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.0770 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 176 GLN B 230 ASN S 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.146746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124036 restraints weight = 13388.533| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.19 r_work: 0.3547 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8956 Z= 0.132 Angle : 0.572 8.794 12136 Z= 0.292 Chirality : 0.042 0.197 1386 Planarity : 0.004 0.056 1524 Dihedral : 4.369 26.817 1216 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.44 % Allowed : 20.61 % Favored : 74.95 % 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: 0.10 (0.26), residues: 1111 helix: 1.34 (0.26), residues: 392 sheet: -0.18 (0.31), residues: 283 loop : -0.87 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 168 TYR 0.032 0.002 TYR S 59 PHE 0.019 0.001 PHE R 204 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8953) covalent geometry : angle 0.57198 (12130) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.96339 ( 6) hydrogen bonds : bond 0.03644 ( 437) hydrogen bonds : angle 4.77033 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 267 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8255 (pt0) cc_final: 0.7972 (pt0) REVERT: A 190 THR cc_start: 0.8552 (t) cc_final: 0.8292 (m) REVERT: A 197 LYS cc_start: 0.8216 (mttm) cc_final: 0.7676 (mtpp) REVERT: A 243 MET cc_start: 0.8662 (tpp) cc_final: 0.8028 (tpp) REVERT: A 249 LEU cc_start: 0.8541 (tp) cc_final: 0.8195 (tp) REVERT: A 252 SER cc_start: 0.8684 (t) cc_final: 0.8361 (p) REVERT: A 271 LYS cc_start: 0.8539 (pttt) cc_final: 0.7889 (pttm) REVERT: A 275 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7798 (mm-30) REVERT: A 330 LYS cc_start: 0.8118 (mppt) cc_final: 0.7698 (mppt) REVERT: B 8 ARG cc_start: 0.8209 (ptp90) cc_final: 0.7930 (ptp-110) REVERT: B 17 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: B 96 ARG cc_start: 0.7817 (mpt90) cc_final: 0.7570 (mpt180) REVERT: B 137 ARG cc_start: 0.7533 (mmm160) cc_final: 0.7259 (mmm160) REVERT: B 171 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7646 (mm) REVERT: B 214 ARG cc_start: 0.8667 (mmt90) cc_final: 0.8440 (mmt90) REVERT: B 221 THR cc_start: 0.8447 (t) cc_final: 0.8150 (m) REVERT: B 251 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7020 (mtm-85) REVERT: B 253 PHE cc_start: 0.8768 (m-80) cc_final: 0.8524 (m-80) REVERT: B 263 THR cc_start: 0.8481 (m) cc_final: 0.8257 (t) REVERT: C 20 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8249 (ttpt) REVERT: C 21 MET cc_start: 0.7812 (ptm) cc_final: 0.7528 (ptm) REVERT: S 11 LEU cc_start: 0.8823 (mp) cc_final: 0.8588 (mm) REVERT: S 57 THR cc_start: 0.8061 (m) cc_final: 0.7788 (p) REVERT: S 63 THR cc_start: 0.8543 (t) cc_final: 0.8271 (m) REVERT: S 79 LEU cc_start: 0.8003 (tm) cc_final: 0.7756 (tp) REVERT: S 180 MET cc_start: 0.6143 (tmm) cc_final: 0.5863 (tmm) REVERT: S 190 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7255 (ptt-90) REVERT: S 205 SER cc_start: 0.8423 (t) cc_final: 0.8077 (t) REVERT: S 231 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7747 (p) REVERT: R 55 MET cc_start: 0.7361 (mtm) cc_final: 0.6727 (mtm) REVERT: R 71 PHE cc_start: 0.7665 (m-10) cc_final: 0.7048 (m-10) REVERT: R 82 PHE cc_start: 0.7497 (t80) cc_final: 0.7000 (t80) REVERT: R 124 LEU cc_start: 0.7392 (tp) cc_final: 0.7125 (tp) REVERT: R 142 ARG cc_start: 0.6575 (ttm110) cc_final: 0.6306 (ttm110) REVERT: R 236 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7533 (mm) REVERT: R 285 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6163 (pm20) REVERT: R 297 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7334 (m) REVERT: R 300 PHE cc_start: 0.7479 (m-80) cc_final: 0.7161 (m-10) outliers start: 42 outliers final: 14 residues processed: 281 average time/residue: 0.4790 time to fit residues: 144.4717 Evaluate side-chains 291 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 270 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 53 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: A 304 GLN B 230 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.145921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.123358 restraints weight = 13256.928| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.14 r_work: 0.3527 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8956 Z= 0.146 Angle : 0.583 8.848 12136 Z= 0.295 Chirality : 0.043 0.194 1386 Planarity : 0.004 0.056 1524 Dihedral : 4.365 27.129 1216 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.76 % Allowed : 21.35 % Favored : 73.89 % 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: 0.08 (0.26), residues: 1111 helix: 1.40 (0.26), residues: 392 sheet: -0.30 (0.30), residues: 286 loop : -0.87 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 168 TYR 0.030 0.002 TYR S 59 PHE 0.019 0.002 PHE R 204 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8953) covalent geometry : angle 0.58297 (12130) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.79937 ( 6) hydrogen bonds : bond 0.03639 ( 437) hydrogen bonds : angle 4.70095 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8281 (pt0) cc_final: 0.7992 (pt0) REVERT: A 190 THR cc_start: 0.8563 (t) cc_final: 0.8264 (m) REVERT: A 197 LYS cc_start: 0.8228 (mttm) cc_final: 0.7678 (mtpp) REVERT: A 243 MET cc_start: 0.8702 (tpp) cc_final: 0.8068 (tpp) REVERT: A 249 LEU cc_start: 0.8563 (tp) cc_final: 0.8226 (tp) REVERT: A 252 SER cc_start: 0.8667 (t) cc_final: 0.8355 (p) REVERT: A 275 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7720 (mt-10) REVERT: A 330 LYS cc_start: 0.8167 (mppt) cc_final: 0.7737 (mppt) REVERT: B 8 ARG cc_start: 0.8235 (ptp90) cc_final: 0.7953 (ptp-110) REVERT: B 50 THR cc_start: 0.8485 (m) cc_final: 0.8215 (t) REVERT: B 96 ARG cc_start: 0.7829 (mpt90) cc_final: 0.7577 (mpt180) REVERT: B 137 ARG cc_start: 0.7521 (mmm160) cc_final: 0.7236 (mmm160) REVERT: B 171 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7771 (mm) REVERT: B 214 ARG cc_start: 0.8672 (mmt90) cc_final: 0.8464 (mmt90) REVERT: B 221 THR cc_start: 0.8450 (t) cc_final: 0.8149 (m) REVERT: B 253 PHE cc_start: 0.8743 (m-80) cc_final: 0.8497 (m-80) REVERT: B 263 THR cc_start: 0.8463 (m) cc_final: 0.8206 (t) REVERT: B 274 THR cc_start: 0.8241 (m) cc_final: 0.8019 (p) REVERT: C 20 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8254 (ttpt) REVERT: C 21 MET cc_start: 0.7797 (ptm) cc_final: 0.7511 (ptm) REVERT: S 11 LEU cc_start: 0.8840 (mp) cc_final: 0.8612 (mm) REVERT: S 57 THR cc_start: 0.8029 (m) cc_final: 0.7726 (p) REVERT: S 63 THR cc_start: 0.8563 (t) cc_final: 0.8309 (m) REVERT: S 79 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7742 (tp) REVERT: S 180 MET cc_start: 0.6112 (tmm) cc_final: 0.5866 (tmm) REVERT: S 192 SER cc_start: 0.8707 (t) cc_final: 0.8439 (p) REVERT: S 205 SER cc_start: 0.8386 (t) cc_final: 0.8076 (t) REVERT: R 55 MET cc_start: 0.7337 (mtm) cc_final: 0.6688 (mtm) REVERT: R 71 PHE cc_start: 0.7750 (m-10) cc_final: 0.7101 (m-10) REVERT: R 82 PHE cc_start: 0.7579 (t80) cc_final: 0.7086 (t80) REVERT: R 112 MET cc_start: 0.5945 (mtp) cc_final: 0.5710 (ttp) REVERT: R 117 MET cc_start: 0.7589 (tmm) cc_final: 0.7381 (tmm) REVERT: R 121 VAL cc_start: 0.7869 (t) cc_final: 0.7483 (p) REVERT: R 124 LEU cc_start: 0.7388 (tp) cc_final: 0.7144 (mt) REVERT: R 142 ARG cc_start: 0.6593 (ttm110) cc_final: 0.6318 (ttm110) REVERT: R 285 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6214 (pm20) REVERT: R 300 PHE cc_start: 0.7504 (m-80) cc_final: 0.7151 (m-10) outliers start: 45 outliers final: 23 residues processed: 280 average time/residue: 0.4820 time to fit residues: 144.7230 Evaluate side-chains 287 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 241 LYS Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.0030 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 75 GLN B 230 ASN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.144348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121129 restraints weight = 13304.598| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.18 r_work: 0.3501 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8956 Z= 0.193 Angle : 0.616 8.381 12136 Z= 0.313 Chirality : 0.044 0.204 1386 Planarity : 0.005 0.056 1524 Dihedral : 4.496 23.668 1216 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.44 % Allowed : 22.09 % Favored : 73.47 % 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: -0.01 (0.26), residues: 1111 helix: 1.37 (0.26), residues: 394 sheet: -0.39 (0.30), residues: 290 loop : -0.96 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 168 TYR 0.026 0.002 TYR S 59 PHE 0.019 0.002 PHE R 204 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8953) covalent geometry : angle 0.61588 (12130) SS BOND : bond 0.00288 ( 3) SS BOND : angle 1.12080 ( 6) hydrogen bonds : bond 0.03778 ( 437) hydrogen bonds : angle 4.74896 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8258 (pt0) cc_final: 0.7954 (pt0) REVERT: A 190 THR cc_start: 0.8560 (t) cc_final: 0.8234 (m) REVERT: A 197 LYS cc_start: 0.8189 (mttm) cc_final: 0.7614 (mtpp) REVERT: A 243 MET cc_start: 0.8753 (tpp) cc_final: 0.8059 (tpp) REVERT: A 275 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7727 (mt-10) REVERT: A 330 LYS cc_start: 0.8217 (mppt) cc_final: 0.7789 (mppt) REVERT: B 8 ARG cc_start: 0.8231 (ptp90) cc_final: 0.7888 (mtm110) REVERT: B 50 THR cc_start: 0.8477 (m) cc_final: 0.8218 (t) REVERT: B 96 ARG cc_start: 0.7854 (mpt90) cc_final: 0.7602 (mpt180) REVERT: B 119 ASN cc_start: 0.8060 (m-40) cc_final: 0.7761 (m-40) REVERT: B 137 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7274 (mmm160) REVERT: B 214 ARG cc_start: 0.8671 (mmt90) cc_final: 0.8453 (mmt90) REVERT: B 221 THR cc_start: 0.8458 (t) cc_final: 0.8168 (m) REVERT: B 253 PHE cc_start: 0.8738 (m-80) cc_final: 0.8417 (m-80) REVERT: B 274 THR cc_start: 0.8340 (m) cc_final: 0.8104 (p) REVERT: C 20 LYS cc_start: 0.8570 (ttpt) cc_final: 0.8273 (ttpt) REVERT: C 21 MET cc_start: 0.7793 (ptm) cc_final: 0.7513 (ptm) REVERT: S 11 LEU cc_start: 0.8891 (mp) cc_final: 0.8656 (mm) REVERT: S 57 THR cc_start: 0.8053 (m) cc_final: 0.7738 (p) REVERT: S 63 THR cc_start: 0.8598 (t) cc_final: 0.8298 (m) REVERT: S 79 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7827 (tp) REVERT: S 87 ARG cc_start: 0.8371 (mtt90) cc_final: 0.8158 (mtm-85) REVERT: S 180 MET cc_start: 0.6298 (tmm) cc_final: 0.5994 (tmm) REVERT: S 192 SER cc_start: 0.8684 (t) cc_final: 0.8405 (p) REVERT: S 205 SER cc_start: 0.8383 (t) cc_final: 0.8081 (t) REVERT: S 223 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7309 (t80) REVERT: R 55 MET cc_start: 0.7343 (mtm) cc_final: 0.6726 (mtm) REVERT: R 71 PHE cc_start: 0.7821 (m-10) cc_final: 0.7222 (m-10) REVERT: R 82 PHE cc_start: 0.7665 (t80) cc_final: 0.7158 (t80) REVERT: R 112 MET cc_start: 0.6048 (mtp) cc_final: 0.5805 (ttp) REVERT: R 121 VAL cc_start: 0.8031 (t) cc_final: 0.7518 (p) REVERT: R 142 ARG cc_start: 0.6656 (ttm110) cc_final: 0.6375 (ttm110) REVERT: R 285 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6285 (pm20) REVERT: R 300 PHE cc_start: 0.7521 (m-80) cc_final: 0.7155 (m-10) outliers start: 42 outliers final: 25 residues processed: 287 average time/residue: 0.4542 time to fit residues: 140.1822 Evaluate side-chains 300 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 272 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 72 ILE Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 241 LYS Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.145714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123072 restraints weight = 13278.913| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.16 r_work: 0.3532 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8956 Z= 0.148 Angle : 0.598 8.225 12136 Z= 0.303 Chirality : 0.043 0.181 1386 Planarity : 0.005 0.056 1524 Dihedral : 4.415 23.897 1216 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.81 % Allowed : 24.74 % Favored : 71.46 % 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: 0.05 (0.25), residues: 1111 helix: 1.45 (0.26), residues: 392 sheet: -0.21 (0.31), residues: 278 loop : -1.05 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 168 TYR 0.025 0.002 TYR S 59 PHE 0.020 0.002 PHE S 68 TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8953) covalent geometry : angle 0.59833 (12130) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.86965 ( 6) hydrogen bonds : bond 0.03570 ( 437) hydrogen bonds : angle 4.72534 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 268 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7946 (ttmm) REVERT: A 33 GLU cc_start: 0.8263 (pt0) cc_final: 0.7990 (pt0) REVERT: A 197 LYS cc_start: 0.8160 (mttm) cc_final: 0.7595 (mtpp) REVERT: A 243 MET cc_start: 0.8715 (tpp) cc_final: 0.8036 (tpp) REVERT: A 252 SER cc_start: 0.8616 (t) cc_final: 0.8334 (p) REVERT: A 271 LYS cc_start: 0.8607 (pttt) cc_final: 0.8340 (pttp) REVERT: A 275 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 330 LYS cc_start: 0.8191 (mppt) cc_final: 0.7754 (mppt) REVERT: B 8 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7888 (mtm110) REVERT: B 17 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: B 50 THR cc_start: 0.8454 (m) cc_final: 0.8184 (t) REVERT: B 96 ARG cc_start: 0.7815 (mpt90) cc_final: 0.7575 (mpt180) REVERT: B 137 ARG cc_start: 0.7542 (mmm160) cc_final: 0.7235 (mmm160) REVERT: B 214 ARG cc_start: 0.8627 (mmt90) cc_final: 0.8416 (mmt90) REVERT: B 221 THR cc_start: 0.8430 (t) cc_final: 0.8151 (m) REVERT: B 253 PHE cc_start: 0.8730 (m-80) cc_final: 0.8427 (m-80) REVERT: B 274 THR cc_start: 0.8241 (m) cc_final: 0.8032 (p) REVERT: C 20 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8279 (ttpt) REVERT: C 21 MET cc_start: 0.7758 (ptm) cc_final: 0.7485 (ptm) REVERT: C 46 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8378 (mtpp) REVERT: S 11 LEU cc_start: 0.8851 (mp) cc_final: 0.8619 (mm) REVERT: S 57 THR cc_start: 0.8019 (m) cc_final: 0.7723 (p) REVERT: S 63 THR cc_start: 0.8475 (t) cc_final: 0.8124 (m) REVERT: S 79 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7770 (tp) REVERT: S 87 ARG cc_start: 0.8372 (mtt90) cc_final: 0.8155 (mtm-85) REVERT: S 180 MET cc_start: 0.6127 (tmm) cc_final: 0.5858 (tmm) REVERT: S 190 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7317 (ptt-90) REVERT: S 192 SER cc_start: 0.8698 (t) cc_final: 0.8411 (p) REVERT: S 205 SER cc_start: 0.8374 (t) cc_final: 0.8054 (t) REVERT: S 223 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.7139 (t80) REVERT: R 55 MET cc_start: 0.7330 (mtm) cc_final: 0.6706 (mtm) REVERT: R 58 LEU cc_start: 0.8065 (mm) cc_final: 0.7504 (tp) REVERT: R 71 PHE cc_start: 0.7845 (m-10) cc_final: 0.7252 (m-10) REVERT: R 82 PHE cc_start: 0.7693 (t80) cc_final: 0.7353 (t80) REVERT: R 112 MET cc_start: 0.6061 (mtp) cc_final: 0.5828 (ttp) REVERT: R 122 LEU cc_start: 0.8150 (mt) cc_final: 0.7901 (mm) REVERT: R 142 ARG cc_start: 0.6652 (ttm110) cc_final: 0.6358 (ttm110) REVERT: R 222 LEU cc_start: 0.7877 (mp) cc_final: 0.7569 (mt) REVERT: R 285 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: R 300 PHE cc_start: 0.7491 (m-80) cc_final: 0.7121 (m-10) outliers start: 36 outliers final: 21 residues processed: 277 average time/residue: 0.4468 time to fit residues: 132.8255 Evaluate side-chains 291 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 266 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 73 ILE Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 96 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.143554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120390 restraints weight = 13342.173| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.19 r_work: 0.3499 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8956 Z= 0.212 Angle : 0.652 8.765 12136 Z= 0.332 Chirality : 0.045 0.194 1386 Planarity : 0.005 0.058 1524 Dihedral : 4.627 24.213 1216 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.49 % Allowed : 25.69 % Favored : 70.82 % 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: -0.05 (0.26), residues: 1111 helix: 1.39 (0.26), residues: 393 sheet: -0.41 (0.30), residues: 288 loop : -1.03 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 168 TYR 0.046 0.002 TYR S 59 PHE 0.017 0.002 PHE R 204 TRP 0.011 0.002 TRP B 339 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 8953) covalent geometry : angle 0.65192 (12130) SS BOND : bond 0.00235 ( 3) SS BOND : angle 1.07945 ( 6) hydrogen bonds : bond 0.03881 ( 437) hydrogen bonds : angle 4.84204 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 0.329 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: A 17 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7951 (ttmm) REVERT: A 33 GLU cc_start: 0.8268 (pt0) cc_final: 0.7974 (pt0) REVERT: A 197 LYS cc_start: 0.8190 (mttm) cc_final: 0.7578 (mtpp) REVERT: A 243 MET cc_start: 0.8765 (tpp) cc_final: 0.8200 (tpp) REVERT: A 275 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 330 LYS cc_start: 0.8248 (mppt) cc_final: 0.7916 (mppt) REVERT: B 8 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7892 (mtm110) REVERT: B 17 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: B 50 THR cc_start: 0.8506 (m) cc_final: 0.8268 (t) REVERT: B 96 ARG cc_start: 0.7878 (mpt90) cc_final: 0.7628 (mpt180) REVERT: B 137 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7298 (mmm160) REVERT: B 214 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8388 (mmt90) REVERT: B 221 THR cc_start: 0.8443 (t) cc_final: 0.8170 (m) REVERT: B 253 PHE cc_start: 0.8756 (m-80) cc_final: 0.8466 (m-80) REVERT: B 274 THR cc_start: 0.8339 (m) cc_final: 0.8073 (p) REVERT: C 20 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8264 (ttpt) REVERT: C 21 MET cc_start: 0.7805 (ptm) cc_final: 0.7534 (ptm) REVERT: S 11 LEU cc_start: 0.8898 (mp) cc_final: 0.8668 (mm) REVERT: S 63 THR cc_start: 0.8465 (t) cc_final: 0.8189 (m) REVERT: S 79 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7808 (tp) REVERT: S 180 MET cc_start: 0.6310 (tmm) cc_final: 0.6031 (tmm) REVERT: S 192 SER cc_start: 0.8673 (t) cc_final: 0.8382 (p) REVERT: S 205 SER cc_start: 0.8324 (t) cc_final: 0.8014 (t) REVERT: S 208 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7744 (mt-10) REVERT: S 223 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.7282 (t80) REVERT: R 55 MET cc_start: 0.7408 (mtm) cc_final: 0.6797 (mtm) REVERT: R 71 PHE cc_start: 0.7755 (m-10) cc_final: 0.7280 (m-10) REVERT: R 82 PHE cc_start: 0.7690 (t80) cc_final: 0.7176 (t80) REVERT: R 112 MET cc_start: 0.6207 (mtp) cc_final: 0.5958 (ttp) REVERT: R 121 VAL cc_start: 0.8067 (t) cc_final: 0.7558 (p) REVERT: R 122 LEU cc_start: 0.8247 (mt) cc_final: 0.7958 (mm) REVERT: R 142 ARG cc_start: 0.6627 (ttm110) cc_final: 0.6332 (ttm110) REVERT: R 222 LEU cc_start: 0.7930 (mp) cc_final: 0.7610 (mt) REVERT: R 236 LEU cc_start: 0.7908 (mt) cc_final: 0.7380 (mp) REVERT: R 285 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6348 (pm20) REVERT: R 300 PHE cc_start: 0.7554 (m-80) cc_final: 0.7176 (m-10) outliers start: 33 outliers final: 21 residues processed: 278 average time/residue: 0.4427 time to fit residues: 132.3824 Evaluate side-chains 288 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.144022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121635 restraints weight = 13249.501| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.13 r_work: 0.3513 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8956 Z= 0.150 Angle : 0.632 9.337 12136 Z= 0.318 Chirality : 0.045 0.327 1386 Planarity : 0.005 0.057 1524 Dihedral : 4.571 24.261 1216 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.17 % Allowed : 26.96 % Favored : 69.87 % 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: -0.00 (0.26), residues: 1111 helix: 1.41 (0.26), residues: 393 sheet: -0.26 (0.31), residues: 278 loop : -1.08 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 168 TYR 0.018 0.002 TYR S 223 PHE 0.016 0.002 PHE R 204 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8953) covalent geometry : angle 0.63159 (12130) SS BOND : bond 0.00232 ( 3) SS BOND : angle 0.97685 ( 6) hydrogen bonds : bond 0.03605 ( 437) hydrogen bonds : angle 4.86062 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 261 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7979 (ttmm) REVERT: A 33 GLU cc_start: 0.8219 (pt0) cc_final: 0.7954 (pt0) REVERT: A 197 LYS cc_start: 0.8197 (mttm) cc_final: 0.7584 (mtpp) REVERT: A 243 MET cc_start: 0.8657 (tpp) cc_final: 0.8087 (tpp) REVERT: A 275 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 330 LYS cc_start: 0.8231 (mppt) cc_final: 0.7890 (mppt) REVERT: B 8 ARG cc_start: 0.8249 (ptp90) cc_final: 0.7934 (mtm110) REVERT: B 50 THR cc_start: 0.8470 (m) cc_final: 0.8208 (t) REVERT: B 96 ARG cc_start: 0.7826 (mpt90) cc_final: 0.7554 (mpt180) REVERT: B 137 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7231 (mmm160) REVERT: B 175 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: B 221 THR cc_start: 0.8408 (t) cc_final: 0.8140 (m) REVERT: B 253 PHE cc_start: 0.8734 (m-80) cc_final: 0.8364 (m-80) REVERT: C 20 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8210 (ttpt) REVERT: C 21 MET cc_start: 0.7758 (ptm) cc_final: 0.7479 (ptm) REVERT: C 46 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8412 (mtpp) REVERT: S 63 THR cc_start: 0.8097 (t) cc_final: 0.7741 (m) REVERT: S 87 ARG cc_start: 0.8370 (mtt180) cc_final: 0.8152 (mtm-85) REVERT: S 180 MET cc_start: 0.6087 (tmm) cc_final: 0.5861 (tmm) REVERT: S 190 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: S 192 SER cc_start: 0.8692 (t) cc_final: 0.8408 (p) REVERT: S 205 SER cc_start: 0.8307 (t) cc_final: 0.8005 (t) REVERT: S 223 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.7091 (t80) REVERT: R 55 MET cc_start: 0.7231 (mtm) cc_final: 0.6656 (mtm) REVERT: R 58 LEU cc_start: 0.8073 (mm) cc_final: 0.7536 (tp) REVERT: R 71 PHE cc_start: 0.7814 (m-10) cc_final: 0.7358 (m-10) REVERT: R 82 PHE cc_start: 0.7731 (t80) cc_final: 0.7471 (t80) REVERT: R 112 MET cc_start: 0.6138 (mtp) cc_final: 0.5902 (ttp) REVERT: R 122 LEU cc_start: 0.8235 (mt) cc_final: 0.7987 (mm) REVERT: R 142 ARG cc_start: 0.6640 (ttm110) cc_final: 0.6338 (ttm110) REVERT: R 222 LEU cc_start: 0.7855 (mp) cc_final: 0.7514 (mt) REVERT: R 236 LEU cc_start: 0.7841 (mt) cc_final: 0.7304 (mp) REVERT: R 285 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: R 300 PHE cc_start: 0.7521 (m-80) cc_final: 0.7154 (m-10) outliers start: 30 outliers final: 14 residues processed: 270 average time/residue: 0.4803 time to fit residues: 139.1212 Evaluate side-chains 272 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 255 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 75 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.144006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121431 restraints weight = 13247.865| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.17 r_work: 0.3495 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8956 Z= 0.180 Angle : 0.647 8.699 12136 Z= 0.327 Chirality : 0.044 0.180 1386 Planarity : 0.005 0.058 1524 Dihedral : 4.557 24.790 1216 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.22 % Allowed : 28.44 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 1111 helix: 1.39 (0.26), residues: 394 sheet: -0.25 (0.31), residues: 280 loop : -1.07 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 168 TYR 0.018 0.002 TYR S 178 PHE 0.016 0.002 PHE R 204 TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 8953) covalent geometry : angle 0.64674 (12130) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.09536 ( 6) hydrogen bonds : bond 0.03659 ( 437) hydrogen bonds : angle 4.91217 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7987 (ttmm) REVERT: A 197 LYS cc_start: 0.8202 (mttm) cc_final: 0.7965 (mtpp) REVERT: A 243 MET cc_start: 0.8632 (tpp) cc_final: 0.8197 (tpp) REVERT: A 250 PHE cc_start: 0.8191 (t80) cc_final: 0.7799 (t80) REVERT: A 275 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 330 LYS cc_start: 0.8253 (mppt) cc_final: 0.7913 (mppt) REVERT: B 8 ARG cc_start: 0.8224 (ptp90) cc_final: 0.7921 (mtm110) REVERT: B 17 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: B 50 THR cc_start: 0.8481 (m) cc_final: 0.8242 (t) REVERT: B 96 ARG cc_start: 0.7856 (mpt90) cc_final: 0.7580 (mpt180) REVERT: B 137 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7259 (mmm160) REVERT: B 214 ARG cc_start: 0.8642 (mmt90) cc_final: 0.8425 (mmt90) REVERT: B 221 THR cc_start: 0.8414 (t) cc_final: 0.8152 (m) REVERT: B 253 PHE cc_start: 0.8751 (m-80) cc_final: 0.8386 (m-80) REVERT: B 274 THR cc_start: 0.8301 (m) cc_final: 0.8067 (p) REVERT: C 20 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8239 (ttpt) REVERT: C 21 MET cc_start: 0.7789 (ptm) cc_final: 0.7514 (ptm) REVERT: C 46 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8446 (mtpp) REVERT: S 63 THR cc_start: 0.8013 (t) cc_final: 0.7704 (m) REVERT: S 68 PHE cc_start: 0.8412 (m-10) cc_final: 0.7623 (m-80) REVERT: S 87 ARG cc_start: 0.8352 (mtt180) cc_final: 0.7825 (mtt90) REVERT: S 180 MET cc_start: 0.6170 (tmm) cc_final: 0.5936 (tmm) REVERT: S 192 SER cc_start: 0.8683 (t) cc_final: 0.8397 (p) REVERT: S 205 SER cc_start: 0.8313 (t) cc_final: 0.8009 (t) REVERT: S 223 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.7165 (t80) REVERT: R 55 MET cc_start: 0.7304 (mtm) cc_final: 0.6749 (mtm) REVERT: R 71 PHE cc_start: 0.7807 (m-10) cc_final: 0.7343 (m-10) REVERT: R 82 PHE cc_start: 0.7736 (t80) cc_final: 0.7517 (t80) REVERT: R 112 MET cc_start: 0.6187 (mtp) cc_final: 0.5949 (ttp) REVERT: R 142 ARG cc_start: 0.6664 (ttm110) cc_final: 0.6368 (ttm110) REVERT: R 285 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: R 300 PHE cc_start: 0.7530 (m-80) cc_final: 0.7147 (m-10) outliers start: 21 outliers final: 14 residues processed: 269 average time/residue: 0.4732 time to fit residues: 136.6941 Evaluate side-chains 274 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 175 LEU Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 285 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.144479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.122335 restraints weight = 13231.837| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.14 r_work: 0.3520 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8956 Z= 0.145 Angle : 0.650 12.470 12136 Z= 0.324 Chirality : 0.044 0.196 1386 Planarity : 0.005 0.057 1524 Dihedral : 4.499 24.891 1216 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.54 % Allowed : 28.44 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 1111 helix: 1.41 (0.26), residues: 394 sheet: -0.20 (0.31), residues: 278 loop : -1.10 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 168 TYR 0.019 0.001 TYR S 223 PHE 0.027 0.002 PHE S 68 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8953) covalent geometry : angle 0.64999 (12130) SS BOND : bond 0.00366 ( 3) SS BOND : angle 0.89423 ( 6) hydrogen bonds : bond 0.03506 ( 437) hydrogen bonds : angle 4.91640 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.96 seconds wall clock time: 68 minutes 23.11 seconds (4103.11 seconds total)