Starting phenix.real_space_refine on Sun May 3 09:58:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nw_75873/05_2026/11nw_75873.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nw_75873/05_2026/11nw_75873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11nw_75873/05_2026/11nw_75873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nw_75873/05_2026/11nw_75873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11nw_75873/05_2026/11nw_75873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nw_75873/05_2026/11nw_75873.map" } resolution = 2.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 3627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12119 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "A" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 401 Classifications: {'water': 401} Link IDs: {None: 400} Chain: "B" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 415 Classifications: {'water': 415} Link IDs: {None: 414} Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 409 Classifications: {'water': 409} Link IDs: {None: 408} Chain: "D" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 422 Classifications: {'water': 422} Link IDs: {None: 421} Time building chain proxies: 3.32, per 1000 atoms: 0.27 Number of scatterers: 12119 At special positions: 0 Unit cell: (102.165, 81.585, 107.31, 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 44 16.00 O 3627 8.00 N 1860 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.23 Conformation dependent library (CDL) restraints added in 439.1 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 54.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.816A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.570A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 258 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.569A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 338 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.743A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.515A pdb=" N GLN B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 35 through 45 removed outlier: 3.796A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.792A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 Processing helix chain 'C' and resid 197 through 219 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.637A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.536A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.758A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.836A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.825A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.490A pdb=" N GLY B 28 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE B 77 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 30 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 187 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.784A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.837A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 576 hydrogen bonds defined for protein. 1662 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: 1.75 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2015 1.33 - 1.45: 2385 1.45 - 1.57: 6216 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" N ASN A 70 " pdb=" CA ASN A 70 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.51e+00 bond pdb=" N VAL D 328 " pdb=" CA VAL D 328 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.14e-02 7.69e+03 9.44e+00 bond pdb=" C LYS B 293 " pdb=" N PRO B 294 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.11e-02 8.12e+03 9.24e+00 bond pdb=" N PHE C 144 " pdb=" CA PHE C 144 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.29e-02 6.01e+03 8.71e+00 bond pdb=" N LYS D 316 " pdb=" CA LYS D 316 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.56e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 13644 1.50 - 3.01: 695 3.01 - 4.51: 92 4.51 - 6.02: 22 6.02 - 7.52: 11 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " pdb=" CG PHE C 144 " ideal model delta sigma weight residual 113.80 118.79 -4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " pdb=" CG PHE D 144 " ideal model delta sigma weight residual 113.80 118.54 -4.74 1.00e+00 1.00e+00 2.25e+01 angle pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " pdb=" CG PHE A 144 " ideal model delta sigma weight residual 113.80 118.50 -4.70 1.00e+00 1.00e+00 2.20e+01 angle pdb=" O PRO B 261 " pdb=" C PRO B 261 " pdb=" N PRO B 262 " ideal model delta sigma weight residual 121.15 119.02 2.13 4.70e-01 4.53e+00 2.05e+01 angle pdb=" N ARG B 68 " pdb=" CA ARG B 68 " pdb=" C ARG B 68 " ideal model delta sigma weight residual 112.38 117.77 -5.39 1.22e+00 6.72e-01 1.95e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6080 17.94 - 35.88: 303 35.88 - 53.82: 75 53.82 - 71.76: 31 71.76 - 89.70: 15 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" C PHE C 144 " pdb=" N PHE C 144 " pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " ideal model delta harmonic sigma weight residual -122.60 -131.16 8.56 0 2.50e+00 1.60e-01 1.17e+01 dihedral pdb=" CA ASP C 67 " pdb=" CB ASP C 67 " pdb=" CG ASP C 67 " pdb=" OD1 ASP C 67 " ideal model delta sinusoidal sigma weight residual -30.00 -88.48 58.48 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" C PHE A 144 " pdb=" N PHE A 144 " pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " ideal model delta harmonic sigma weight residual -122.60 -130.91 8.31 0 2.50e+00 1.60e-01 1.10e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1190 0.045 - 0.090: 296 0.090 - 0.135: 127 0.135 - 0.180: 19 0.180 - 0.225: 12 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA LEU D 305 " pdb=" N LEU D 305 " pdb=" C LEU D 305 " pdb=" CB LEU D 305 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE A 190 " pdb=" N ILE A 190 " pdb=" C ILE A 190 " pdb=" CB ILE A 190 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE B 185 " pdb=" N ILE B 185 " pdb=" C ILE B 185 " pdb=" CB ILE B 185 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 144 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C PHE C 144 " -0.048 2.00e-02 2.50e+03 pdb=" O PHE C 144 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA C 145 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 292 " -0.013 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C LEU B 292 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU B 292 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS B 293 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 259 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C THR D 259 " 0.037 2.00e-02 2.50e+03 pdb=" O THR D 259 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL D 260 " -0.013 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3449 2.80 - 3.33: 12707 3.33 - 3.85: 24433 3.85 - 4.38: 28916 4.38 - 4.90: 44527 Nonbonded interactions: 114032 Sorted by model distance: nonbonded pdb=" O GLN C 60 " pdb=" OG1 THR C 64 " model vdw 2.275 3.040 nonbonded pdb=" OE1 GLU B 121 " pdb=" OG SER B 159 " model vdw 2.296 3.040 nonbonded pdb=" O ARG D 42 " pdb=" OG SER D 45 " model vdw 2.300 3.040 nonbonded pdb=" O HOH B 674 " pdb=" O HOH B 782 " model vdw 2.301 3.040 nonbonded pdb=" O HOH C 536 " pdb=" O HOH C 662 " model vdw 2.301 3.040 ... (remaining 114027 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 5.000 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.210 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10672 Z= 0.321 Angle : 0.741 7.519 14464 Z= 0.487 Chirality : 0.051 0.225 1644 Planarity : 0.005 0.057 1880 Dihedral : 13.131 89.701 3984 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.81 % Allowed : 0.90 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 0.90 (0.23), residues: 1364 helix: 1.36 (0.19), residues: 740 sheet: -1.39 (0.36), residues: 200 loop : 0.54 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.025 0.002 TYR A 84 PHE 0.027 0.002 PHE C 144 TRP 0.024 0.004 TRP D 147 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00453 (10672) covalent geometry : angle 0.74134 (14464) hydrogen bonds : bond 0.14542 ( 576) hydrogen bonds : angle 5.86237 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.458 Fit side-chains REVERT: A 95 GLN cc_start: 0.8349 (tt0) cc_final: 0.7615 (tp-100) REVERT: A 152 LYS cc_start: 0.8560 (tttp) cc_final: 0.8120 (tptp) REVERT: A 155 GLU cc_start: 0.6236 (pm20) cc_final: 0.5995 (pm20) REVERT: A 193 ASP cc_start: 0.8438 (m-30) cc_final: 0.8225 (m-30) REVERT: A 199 LYS cc_start: 0.8434 (mtmt) cc_final: 0.7738 (pptt) REVERT: A 242 LYS cc_start: 0.8384 (mttt) cc_final: 0.7890 (mmtm) REVERT: A 246 GLU cc_start: 0.8237 (mp0) cc_final: 0.8030 (mp0) REVERT: A 325 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6758 (mm-30) REVERT: B 237 HIS cc_start: 0.7946 (t70) cc_final: 0.7475 (m-70) REVERT: B 242 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7397 (tptm) REVERT: B 303 ARG cc_start: 0.6962 (ttp-170) cc_final: 0.6670 (mtp85) REVERT: C 199 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8244 (mttm) REVERT: C 288 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8162 (mttm) REVERT: C 303 ARG cc_start: 0.7431 (ttm170) cc_final: 0.7213 (mtm180) REVERT: D 42 ARG cc_start: 0.6496 (mtp180) cc_final: 0.6203 (mmp-170) REVERT: D 237 HIS cc_start: 0.7747 (t-90) cc_final: 0.7228 (m-70) REVERT: D 242 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7737 (mtpt) REVERT: D 303 ARG cc_start: 0.7339 (ttp80) cc_final: 0.6811 (mtp85) outliers start: 9 outliers final: 4 residues processed: 168 average time/residue: 0.8970 time to fit residues: 159.3119 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 241 GLN A 287 ASN A 339 GLN C 95 GLN C 136 GLN C 231 ASN C 241 GLN D 60 GLN D 85 GLN D 95 GLN D 219 HIS D 339 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110020 restraints weight = 10382.597| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.07 r_work: 0.3120 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10672 Z= 0.140 Angle : 0.546 5.981 14464 Z= 0.293 Chirality : 0.043 0.147 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.501 58.381 1480 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.53 % Allowed : 6.21 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.59 (0.23), residues: 1364 helix: 2.09 (0.19), residues: 744 sheet: -1.06 (0.32), residues: 248 loop : 0.66 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 172 TYR 0.019 0.002 TYR A 213 PHE 0.018 0.002 PHE B 144 TRP 0.018 0.002 TRP D 147 HIS 0.008 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00298 (10672) covalent geometry : angle 0.54591 (14464) hydrogen bonds : bond 0.05885 ( 576) hydrogen bonds : angle 4.57852 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.8393 (tt0) cc_final: 0.7726 (tp-100) REVERT: A 246 GLU cc_start: 0.8298 (mp0) cc_final: 0.8045 (mp0) REVERT: A 325 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7222 (mm-30) REVERT: B 139 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8214 (ptmt) REVERT: B 199 LYS cc_start: 0.8272 (mmpt) cc_final: 0.7968 (mmtm) REVERT: B 237 HIS cc_start: 0.7898 (t70) cc_final: 0.7505 (m-70) REVERT: B 242 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7408 (tptm) REVERT: B 303 ARG cc_start: 0.7009 (ttp-170) cc_final: 0.6734 (mtp85) REVERT: B 311 LYS cc_start: 0.7902 (tttm) cc_final: 0.7491 (ttpp) REVERT: C 42 ARG cc_start: 0.6778 (mtp180) cc_final: 0.6532 (mpt-90) REVERT: C 199 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8312 (mttm) REVERT: D 13 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8522 (tttp) REVERT: D 42 ARG cc_start: 0.6764 (mtp180) cc_final: 0.6318 (mmm160) REVERT: D 237 HIS cc_start: 0.7649 (t-90) cc_final: 0.7100 (m-70) REVERT: D 242 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7637 (mtpt) REVERT: D 303 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7020 (mtp85) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 0.9000 time to fit residues: 110.6681 Evaluate side-chains 101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 HIS A 241 GLN B 287 ASN C 4 HIS C 241 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.110393 restraints weight = 10459.869| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.06 r_work: 0.3125 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10672 Z= 0.124 Angle : 0.505 5.850 14464 Z= 0.270 Chirality : 0.041 0.149 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.429 57.970 1480 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 6.92 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.81 (0.23), residues: 1364 helix: 2.29 (0.19), residues: 744 sheet: -0.89 (0.33), residues: 228 loop : 0.54 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 68 TYR 0.019 0.002 TYR A 213 PHE 0.016 0.001 PHE B 144 TRP 0.012 0.002 TRP D 147 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00262 (10672) covalent geometry : angle 0.50452 (14464) hydrogen bonds : bond 0.05434 ( 576) hydrogen bonds : angle 4.38757 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.478 Fit side-chains REVERT: A 38 SER cc_start: 0.8567 (t) cc_final: 0.8334 (m) REVERT: A 95 GLN cc_start: 0.8373 (tt0) cc_final: 0.7687 (tp-100) REVERT: A 246 GLU cc_start: 0.8245 (mp0) cc_final: 0.7988 (mp0) REVERT: A 325 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 107 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8184 (tmmm) REVERT: B 139 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8022 (ptmt) REVERT: B 173 TYR cc_start: 0.9367 (OUTLIER) cc_final: 0.8264 (t80) REVERT: B 237 HIS cc_start: 0.7836 (t70) cc_final: 0.7416 (m-70) REVERT: B 242 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7675 (mttt) REVERT: B 303 ARG cc_start: 0.6993 (ttp-170) cc_final: 0.6573 (mtp85) REVERT: B 311 LYS cc_start: 0.7874 (tttm) cc_final: 0.7461 (ttpp) REVERT: C 42 ARG cc_start: 0.6780 (mtp180) cc_final: 0.6544 (mpt-90) REVERT: C 86 LYS cc_start: 0.8393 (mttp) cc_final: 0.8045 (mttm) REVERT: C 199 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8244 (mttm) REVERT: D 13 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8464 (tttp) REVERT: D 42 ARG cc_start: 0.6692 (mtp180) cc_final: 0.6320 (mmm160) REVERT: D 173 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.9005 (t80) REVERT: D 237 HIS cc_start: 0.7671 (t-90) cc_final: 0.7138 (m-70) REVERT: D 242 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7644 (mtpt) outliers start: 22 outliers final: 10 residues processed: 115 average time/residue: 0.8534 time to fit residues: 104.4468 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 119 ASN C 4 HIS C 95 GLN C 168 ASN C 241 GLN D 60 GLN D 95 GLN D 180 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108235 restraints weight = 10469.858| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.22 r_work: 0.3101 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10672 Z= 0.110 Angle : 0.478 6.167 14464 Z= 0.254 Chirality : 0.040 0.148 1644 Planarity : 0.003 0.031 1880 Dihedral : 5.292 57.973 1480 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.71 % Allowed : 8.00 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.88 (0.23), residues: 1364 helix: 2.38 (0.19), residues: 752 sheet: -0.93 (0.33), residues: 228 loop : 0.50 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 303 TYR 0.018 0.002 TYR C 213 PHE 0.015 0.001 PHE B 144 TRP 0.010 0.002 TRP D 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00233 (10672) covalent geometry : angle 0.47845 (14464) hydrogen bonds : bond 0.04881 ( 576) hydrogen bonds : angle 4.23427 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.480 Fit side-chains REVERT: A 38 SER cc_start: 0.8513 (t) cc_final: 0.8271 (m) REVERT: A 52 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: A 95 GLN cc_start: 0.8364 (tt0) cc_final: 0.7587 (tp-100) REVERT: A 246 GLU cc_start: 0.8213 (mp0) cc_final: 0.7937 (mp0) REVERT: A 311 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7079 (ttpp) REVERT: A 321 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7374 (mmtm) REVERT: A 325 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7131 (mm-30) REVERT: B 165 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: B 173 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.8125 (t80) REVERT: B 199 LYS cc_start: 0.8140 (mmpt) cc_final: 0.7805 (mmtt) REVERT: B 237 HIS cc_start: 0.7789 (t70) cc_final: 0.7280 (m-70) REVERT: B 242 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7631 (mttt) REVERT: B 303 ARG cc_start: 0.6878 (ttp-170) cc_final: 0.6470 (ttp-170) REVERT: B 311 LYS cc_start: 0.7771 (tttm) cc_final: 0.7341 (ttpp) REVERT: C 42 ARG cc_start: 0.6740 (mtp180) cc_final: 0.6417 (mpt-90) REVERT: C 86 LYS cc_start: 0.8331 (mttp) cc_final: 0.7935 (mttm) REVERT: D 42 ARG cc_start: 0.6636 (mtp180) cc_final: 0.6192 (mmm160) REVERT: D 173 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8979 (t80) REVERT: D 237 HIS cc_start: 0.7615 (t-90) cc_final: 0.6969 (m-70) REVERT: D 242 LYS cc_start: 0.7952 (mmtt) cc_final: 0.7548 (mtpt) outliers start: 19 outliers final: 7 residues processed: 110 average time/residue: 0.8703 time to fit residues: 101.6760 Evaluate side-chains 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 114 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 4 HIS C 95 GLN C 241 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.140366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108879 restraints weight = 10433.454| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.06 r_work: 0.3104 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10672 Z= 0.135 Angle : 0.518 6.150 14464 Z= 0.277 Chirality : 0.042 0.153 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.460 57.482 1480 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.25 % Allowed : 7.91 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.84 (0.23), residues: 1364 helix: 2.36 (0.19), residues: 744 sheet: -0.94 (0.33), residues: 228 loop : 0.49 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.024 0.002 TYR A 213 PHE 0.017 0.002 PHE A 144 TRP 0.012 0.002 TRP D 147 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00293 (10672) covalent geometry : angle 0.51830 (14464) hydrogen bonds : bond 0.05724 ( 576) hydrogen bonds : angle 4.31879 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.480 Fit side-chains REVERT: A 38 SER cc_start: 0.8605 (t) cc_final: 0.8397 (m) REVERT: A 52 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: A 95 GLN cc_start: 0.8353 (tt0) cc_final: 0.7673 (tp-100) REVERT: A 246 GLU cc_start: 0.8237 (mp0) cc_final: 0.7981 (mp0) REVERT: A 311 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7181 (ttpp) REVERT: A 321 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7589 (mmtm) REVERT: A 325 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7204 (mm-30) REVERT: B 52 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: B 139 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8007 (ptmt) REVERT: B 173 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.8229 (t80) REVERT: B 199 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7865 (mmtm) REVERT: B 237 HIS cc_start: 0.7830 (t70) cc_final: 0.7398 (m-70) REVERT: B 242 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7692 (mttt) REVERT: B 303 ARG cc_start: 0.7025 (ttp-170) cc_final: 0.6592 (mtp85) REVERT: B 311 LYS cc_start: 0.7917 (tttm) cc_final: 0.7533 (ttpp) REVERT: C 42 ARG cc_start: 0.6808 (mtp180) cc_final: 0.6545 (mpt-90) REVERT: C 86 LYS cc_start: 0.8387 (mttp) cc_final: 0.8037 (mttm) REVERT: D 13 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8488 (tttp) REVERT: D 14 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: D 42 ARG cc_start: 0.6656 (mtp180) cc_final: 0.6273 (mmm160) REVERT: D 237 HIS cc_start: 0.7684 (t-90) cc_final: 0.7157 (m-70) REVERT: D 242 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7619 (mtpt) outliers start: 25 outliers final: 11 residues processed: 112 average time/residue: 0.8475 time to fit residues: 101.0584 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 37 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 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 241 GLN C 4 HIS C 95 GLN C 241 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110175 restraints weight = 10369.129| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.06 r_work: 0.3124 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10672 Z= 0.118 Angle : 0.490 5.802 14464 Z= 0.261 Chirality : 0.041 0.150 1644 Planarity : 0.003 0.032 1880 Dihedral : 5.356 57.471 1480 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.07 % Allowed : 8.45 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.85 (0.23), residues: 1364 helix: 2.38 (0.19), residues: 752 sheet: -0.98 (0.33), residues: 228 loop : 0.45 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.020 0.002 TYR A 213 PHE 0.016 0.001 PHE A 144 TRP 0.009 0.002 TRP C 147 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00251 (10672) covalent geometry : angle 0.49039 (14464) hydrogen bonds : bond 0.05199 ( 576) hydrogen bonds : angle 4.24629 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.463 Fit side-chains REVERT: A 38 SER cc_start: 0.8596 (t) cc_final: 0.8390 (m) REVERT: A 52 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: A 95 GLN cc_start: 0.8366 (tt0) cc_final: 0.7657 (tp-100) REVERT: A 246 GLU cc_start: 0.8228 (mp0) cc_final: 0.7974 (mp0) REVERT: A 311 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7178 (ttpp) REVERT: A 316 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7212 (ptpt) REVERT: A 321 LYS cc_start: 0.7823 (tppt) cc_final: 0.7585 (mmtm) REVERT: A 325 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7196 (mm-30) REVERT: B 41 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7512 (mmtp) REVERT: B 52 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: B 139 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7906 (ptmt) REVERT: B 173 TYR cc_start: 0.9357 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 199 LYS cc_start: 0.8193 (mmpt) cc_final: 0.7884 (mmtm) REVERT: B 237 HIS cc_start: 0.7843 (t70) cc_final: 0.7430 (m-70) REVERT: B 242 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7665 (mttt) REVERT: B 303 ARG cc_start: 0.6990 (ttp-170) cc_final: 0.6561 (mtp85) REVERT: B 311 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7481 (ttpp) REVERT: B 316 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7192 (ptpp) REVERT: C 42 ARG cc_start: 0.6839 (mtp180) cc_final: 0.6558 (mpt-90) REVERT: C 86 LYS cc_start: 0.8382 (mttp) cc_final: 0.8035 (mttm) REVERT: D 13 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8451 (tttp) REVERT: D 14 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: D 42 ARG cc_start: 0.6657 (mtp180) cc_final: 0.6282 (mmm160) REVERT: D 237 HIS cc_start: 0.7655 (t-90) cc_final: 0.7127 (m-70) REVERT: D 242 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7666 (mtpt) outliers start: 23 outliers final: 9 residues processed: 106 average time/residue: 0.8701 time to fit residues: 97.9805 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 4 HIS C 95 GLN C 241 GLN D 60 GLN D 95 GLN D 136 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.139815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108207 restraints weight = 10346.393| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.06 r_work: 0.3097 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.138 Angle : 0.524 6.269 14464 Z= 0.279 Chirality : 0.042 0.153 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.497 57.456 1480 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.34 % Allowed : 8.36 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.80 (0.23), residues: 1364 helix: 2.35 (0.19), residues: 744 sheet: -1.01 (0.33), residues: 228 loop : 0.47 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 303 TYR 0.025 0.002 TYR A 213 PHE 0.017 0.002 PHE A 144 TRP 0.011 0.002 TRP C 147 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00300 (10672) covalent geometry : angle 0.52400 (14464) hydrogen bonds : bond 0.05825 ( 576) hydrogen bonds : angle 4.34237 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.462 Fit side-chains REVERT: A 38 SER cc_start: 0.8617 (t) cc_final: 0.8409 (m) REVERT: A 52 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: A 95 GLN cc_start: 0.8330 (tt0) cc_final: 0.7644 (tp-100) REVERT: A 246 GLU cc_start: 0.8246 (mp0) cc_final: 0.7979 (mp0) REVERT: A 311 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7212 (ttpp) REVERT: A 316 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7257 (ptpt) REVERT: A 321 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7585 (mmtm) REVERT: A 325 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7192 (mm-30) REVERT: B 41 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7512 (mmtp) REVERT: B 139 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8037 (ptmt) REVERT: B 173 TYR cc_start: 0.9378 (OUTLIER) cc_final: 0.8342 (t80) REVERT: B 199 LYS cc_start: 0.8211 (mmpt) cc_final: 0.7893 (mppt) REVERT: B 237 HIS cc_start: 0.7859 (t70) cc_final: 0.7425 (m-70) REVERT: B 242 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7689 (mttt) REVERT: B 303 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6616 (mtp85) REVERT: B 311 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7566 (ttpp) REVERT: B 316 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7225 (ptpp) REVERT: C 42 ARG cc_start: 0.6851 (mtp180) cc_final: 0.6563 (mpt-90) REVERT: C 86 LYS cc_start: 0.8404 (mttp) cc_final: 0.8058 (mttm) REVERT: D 13 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8501 (tttp) REVERT: D 14 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: D 42 ARG cc_start: 0.6642 (mtp180) cc_final: 0.6280 (mmm160) REVERT: D 237 HIS cc_start: 0.7700 (t-90) cc_final: 0.7180 (m-70) REVERT: D 242 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7687 (mtpt) outliers start: 26 outliers final: 9 residues processed: 106 average time/residue: 0.9258 time to fit residues: 104.0751 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 4 HIS C 95 GLN C 241 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110933 restraints weight = 10340.089| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.06 r_work: 0.3136 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10672 Z= 0.110 Angle : 0.479 5.633 14464 Z= 0.254 Chirality : 0.040 0.150 1644 Planarity : 0.003 0.032 1880 Dihedral : 5.293 57.515 1480 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.98 % Allowed : 8.72 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.89 (0.23), residues: 1364 helix: 2.43 (0.19), residues: 752 sheet: -0.99 (0.33), residues: 228 loop : 0.45 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 303 TYR 0.018 0.002 TYR A 213 PHE 0.015 0.001 PHE B 144 TRP 0.008 0.001 TRP D 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00233 (10672) covalent geometry : angle 0.47876 (14464) hydrogen bonds : bond 0.04923 ( 576) hydrogen bonds : angle 4.20174 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.474 Fit side-chains REVERT: A 38 SER cc_start: 0.8579 (t) cc_final: 0.8372 (m) REVERT: A 52 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 95 GLN cc_start: 0.8359 (tt0) cc_final: 0.7654 (tp-100) REVERT: A 246 GLU cc_start: 0.8233 (mp0) cc_final: 0.7978 (mp0) REVERT: A 311 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7188 (ttpp) REVERT: A 316 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7216 (ptpt) REVERT: A 321 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7568 (mmtm) REVERT: A 325 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7206 (mm-30) REVERT: B 41 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7481 (mmtp) REVERT: B 173 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.8131 (t80) REVERT: B 199 LYS cc_start: 0.8202 (mmpt) cc_final: 0.7887 (mmtm) REVERT: B 237 HIS cc_start: 0.7836 (t70) cc_final: 0.7420 (m-70) REVERT: B 242 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7663 (mttt) REVERT: B 303 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.6595 (ttp-170) REVERT: B 311 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7476 (ttpp) REVERT: C 42 ARG cc_start: 0.6799 (mtp180) cc_final: 0.6537 (mpt-90) REVERT: C 86 LYS cc_start: 0.8392 (mttp) cc_final: 0.8040 (mttm) REVERT: D 13 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8410 (tttp) REVERT: D 14 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: D 42 ARG cc_start: 0.6624 (mtp180) cc_final: 0.6338 (mmp-170) REVERT: D 173 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8877 (t80) REVERT: D 237 HIS cc_start: 0.7655 (t-90) cc_final: 0.7133 (m-70) REVERT: D 242 LYS cc_start: 0.8006 (mmtt) cc_final: 0.7685 (mtpt) REVERT: D 311 LYS cc_start: 0.8001 (tttm) cc_final: 0.7639 (ttpp) outliers start: 22 outliers final: 9 residues processed: 106 average time/residue: 0.9167 time to fit residues: 103.0819 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 4 HIS C 95 GLN C 241 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107646 restraints weight = 10279.805| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.05 r_work: 0.3089 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10672 Z= 0.148 Angle : 0.539 6.467 14464 Z= 0.288 Chirality : 0.043 0.154 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.538 57.411 1480 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 8.63 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.79 (0.23), residues: 1364 helix: 2.33 (0.19), residues: 744 sheet: -1.41 (0.37), residues: 180 loop : 0.49 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.026 0.002 TYR A 213 PHE 0.017 0.002 PHE A 144 TRP 0.012 0.002 TRP D 147 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00323 (10672) covalent geometry : angle 0.53925 (14464) hydrogen bonds : bond 0.06054 ( 576) hydrogen bonds : angle 4.37261 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.496 Fit side-chains REVERT: A 38 SER cc_start: 0.8609 (t) cc_final: 0.8400 (m) REVERT: A 52 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: A 95 GLN cc_start: 0.8343 (tt0) cc_final: 0.7650 (tp-100) REVERT: A 246 GLU cc_start: 0.8292 (mp0) cc_final: 0.8038 (mp0) REVERT: A 311 LYS cc_start: 0.7948 (ttpt) cc_final: 0.7205 (ttpp) REVERT: A 316 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7231 (ptpt) REVERT: A 321 LYS cc_start: 0.7847 (tppt) cc_final: 0.7596 (mmtm) REVERT: A 325 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 139 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8050 (ptmt) REVERT: B 173 TYR cc_start: 0.9381 (OUTLIER) cc_final: 0.8336 (t80) REVERT: B 237 HIS cc_start: 0.7862 (t70) cc_final: 0.7427 (m-70) REVERT: B 242 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7693 (mttt) REVERT: B 303 ARG cc_start: 0.7073 (ttp-170) cc_final: 0.6632 (mtp85) REVERT: B 311 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7575 (ttpp) REVERT: C 42 ARG cc_start: 0.6849 (mtp180) cc_final: 0.6597 (mpt-90) REVERT: C 86 LYS cc_start: 0.8409 (mttp) cc_final: 0.8051 (mttm) REVERT: D 13 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8489 (tttp) REVERT: D 14 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.7740 (tm-30) REVERT: D 42 ARG cc_start: 0.6613 (mtp180) cc_final: 0.6327 (mmp-170) REVERT: D 237 HIS cc_start: 0.7703 (t-90) cc_final: 0.7166 (m-70) REVERT: D 242 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7700 (mtpt) REVERT: D 311 LYS cc_start: 0.8042 (tttm) cc_final: 0.7676 (ttpp) outliers start: 21 outliers final: 9 residues processed: 106 average time/residue: 0.9095 time to fit residues: 102.3187 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 8 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN C 4 HIS C 95 GLN C 241 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110323 restraints weight = 10422.078| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.04 r_work: 0.3125 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10672 Z= 0.113 Angle : 0.489 6.597 14464 Z= 0.258 Chirality : 0.041 0.150 1644 Planarity : 0.003 0.032 1880 Dihedral : 5.311 57.421 1480 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.53 % Allowed : 9.17 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.95 (0.23), residues: 1364 helix: 2.49 (0.19), residues: 744 sheet: -0.99 (0.33), residues: 228 loop : 0.51 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.019 0.002 TYR A 213 PHE 0.016 0.001 PHE A 144 TRP 0.008 0.001 TRP B 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00242 (10672) covalent geometry : angle 0.48885 (14464) hydrogen bonds : bond 0.04988 ( 576) hydrogen bonds : angle 4.20917 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.489 Fit side-chains REVERT: A 52 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: A 95 GLN cc_start: 0.8385 (tt0) cc_final: 0.7693 (tp-100) REVERT: A 246 GLU cc_start: 0.8292 (mp0) cc_final: 0.8047 (mp0) REVERT: A 311 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7235 (ttpp) REVERT: A 321 LYS cc_start: 0.7830 (tppt) cc_final: 0.7618 (mmtm) REVERT: A 325 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 173 TYR cc_start: 0.9366 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 199 LYS cc_start: 0.8235 (mmpt) cc_final: 0.7908 (mmtt) REVERT: B 237 HIS cc_start: 0.7874 (t70) cc_final: 0.7487 (m-70) REVERT: B 242 LYS cc_start: 0.8018 (mmtm) cc_final: 0.7701 (mttt) REVERT: B 303 ARG cc_start: 0.7024 (ttp-170) cc_final: 0.6606 (mtp85) REVERT: B 311 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7509 (ttpp) REVERT: C 42 ARG cc_start: 0.6874 (mtp180) cc_final: 0.6615 (mpt-90) REVERT: C 86 LYS cc_start: 0.8421 (mttp) cc_final: 0.8094 (mttm) REVERT: D 13 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8424 (tttp) REVERT: D 14 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: D 42 ARG cc_start: 0.6653 (mtp180) cc_final: 0.6368 (mmp-170) REVERT: D 107 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8697 (ttmm) REVERT: D 237 HIS cc_start: 0.7690 (t-90) cc_final: 0.7206 (m-70) REVERT: D 242 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7743 (mtpt) REVERT: D 311 LYS cc_start: 0.8020 (tttm) cc_final: 0.7664 (ttpp) REVERT: D 329 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8543 (mtpp) outliers start: 17 outliers final: 9 residues processed: 104 average time/residue: 0.9145 time to fit residues: 100.6599 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 14 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 319 ASN C 4 HIS C 95 GLN C 241 GLN D 60 GLN D 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.110188 restraints weight = 10298.975| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.04 r_work: 0.3123 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10672 Z= 0.115 Angle : 0.491 6.698 14464 Z= 0.259 Chirality : 0.041 0.149 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.304 57.533 1480 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.80 % Allowed : 8.81 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 are not related in a simple way. whole: 1.86 (0.23), residues: 1364 helix: 2.43 (0.19), residues: 752 sheet: -1.09 (0.32), residues: 248 loop : 0.56 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 303 TYR 0.020 0.002 TYR A 213 PHE 0.016 0.001 PHE A 144 TRP 0.009 0.001 TRP C 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00246 (10672) covalent geometry : angle 0.49125 (14464) hydrogen bonds : bond 0.05061 ( 576) hydrogen bonds : angle 4.19275 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4730.05 seconds wall clock time: 81 minutes 36.46 seconds (4896.46 seconds total)