Starting phenix.real_space_refine on Sun May 3 10:16:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nx_75874/05_2026/11nx_75874.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nx_75874/05_2026/11nx_75874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nx_75874/05_2026/11nx_75874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nx_75874/05_2026/11nx_75874.map" model { file = "/net/cci-nas-00/data/ceres_data/11nx_75874/05_2026/11nx_75874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nx_75874/05_2026/11nx_75874.cif" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 3774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 12266 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: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 447 Classifications: {'water': 447} Link IDs: {None: 446} Chain: "B" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 448 Classifications: {'water': 448} Link IDs: {None: 447} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 445 Classifications: {'water': 445} Link IDs: {None: 444} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 454 Classifications: {'water': 454} Link IDs: {None: 453} Time building chain proxies: 3.72, per 1000 atoms: 0.30 Number of scatterers: 12266 At special positions: 0 Unit cell: (97.755, 84.525, 106.575, 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 3774 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: 1.12 Conformation dependent library (CDL) restraints added in 390.5 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 55.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.691A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.798A 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 removed outlier: 3.807A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) 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 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 260 removed outlier: 3.573A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 6.229A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.203A 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: 3.730A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.821A 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 79 through 84 removed outlier: 3.745A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) 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 removed outlier: 3.573A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.368A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.006A 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: 3.692A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.822A 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 225 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.571A 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: 6.359A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.009A 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: 3.702A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.798A 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 removed outlier: 3.589A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 6.283A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) 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: 6.808A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.398A 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: 6.796A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.396A 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 32 removed outlier: 6.776A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.410A 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 32 removed outlier: 6.783A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.411A 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 114 596 hydrogen bonds defined for protein. 1722 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: 2.22 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1953 1.32 - 1.45: 2438 1.45 - 1.57: 6225 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" N ILE B 22 " pdb=" CA ILE B 22 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.44e+00 bond pdb=" N ILE C 286 " pdb=" CA ILE C 286 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.39e+00 bond pdb=" N ILE C 22 " pdb=" CA ILE C 22 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.39e+00 bond pdb=" N ILE D 22 " pdb=" CA ILE D 22 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.35e+00 bond pdb=" N ILE D 286 " pdb=" CA ILE D 286 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.33e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 12967 1.26 - 2.52: 1089 2.52 - 3.77: 333 3.77 - 5.03: 59 5.03 - 6.29: 16 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " pdb=" CG PHE D 144 " ideal model delta sigma weight residual 113.80 118.11 -4.31 1.00e+00 1.00e+00 1.86e+01 angle pdb=" C PRO D 262 " pdb=" CA PRO D 262 " pdb=" CB PRO D 262 " ideal model delta sigma weight residual 111.85 105.77 6.08 1.42e+00 4.96e-01 1.83e+01 angle pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " pdb=" CG PHE A 144 " ideal model delta sigma weight residual 113.80 118.01 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " pdb=" CG PHE C 144 " ideal model delta sigma weight residual 113.80 117.97 -4.17 1.00e+00 1.00e+00 1.74e+01 angle pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " pdb=" CG PHE B 144 " ideal model delta sigma weight residual 113.80 117.78 -3.98 1.00e+00 1.00e+00 1.58e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6027 17.67 - 35.34: 332 35.34 - 53.00: 88 53.00 - 70.67: 42 70.67 - 88.34: 15 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA PHE D 299 " pdb=" C PHE D 299 " pdb=" N SER D 300 " pdb=" CA SER D 300 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE B 299 " pdb=" C PHE B 299 " pdb=" N SER B 300 " pdb=" CA SER B 300 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE C 299 " pdb=" C PHE C 299 " pdb=" N SER C 300 " pdb=" CA SER C 300 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1204 0.052 - 0.104: 295 0.104 - 0.156: 110 0.156 - 0.208: 29 0.208 - 0.260: 6 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA LYS C 329 " pdb=" N LYS C 329 " pdb=" C LYS C 329 " pdb=" CB LYS C 329 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ILE D 190 " pdb=" N ILE D 190 " pdb=" C ILE D 190 " pdb=" CB ILE D 190 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+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 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 292 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C LEU A 292 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 292 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 293 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 326 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C GLU A 326 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 326 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 327 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 331 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ALA B 331 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA B 331 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU B 332 " -0.012 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3990 2.82 - 3.34: 13475 3.34 - 3.86: 25050 3.86 - 4.38: 29023 4.38 - 4.90: 45059 Nonbonded interactions: 116597 Sorted by model distance: nonbonded pdb=" O GLN D 60 " pdb=" OG1 THR D 64 " model vdw 2.296 3.040 nonbonded pdb=" O GLN C 60 " pdb=" OG1 THR C 64 " model vdw 2.299 3.040 nonbonded pdb=" O ALA A 87 " pdb=" O HOH A 401 " model vdw 2.300 3.040 nonbonded pdb=" O HOH D 673 " pdb=" O HOH D 830 " model vdw 2.301 3.040 nonbonded pdb=" O HOH C 664 " pdb=" O HOH C 821 " model vdw 2.301 3.040 ... (remaining 116592 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.160 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 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 0.043 10672 Z= 0.397 Angle : 0.848 6.290 14464 Z= 0.580 Chirality : 0.057 0.260 1644 Planarity : 0.005 0.032 1880 Dihedral : 13.892 88.341 3984 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % 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: 0.83 (0.23), residues: 1364 helix: 1.25 (0.19), residues: 708 sheet: -1.15 (0.35), residues: 212 loop : 0.56 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 258 TYR 0.023 0.002 TYR B 213 PHE 0.021 0.002 PHE D 144 TRP 0.021 0.004 TRP A 147 HIS 0.005 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00544 (10672) covalent geometry : angle 0.84760 (14464) hydrogen bonds : bond 0.15096 ( 596) hydrogen bonds : angle 6.43849 ( 1722) *********************** 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 145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.494 Fit side-chains REVERT: A 195 ASP cc_start: 0.7995 (p0) cc_final: 0.7787 (p0) REVERT: A 199 LYS cc_start: 0.8703 (mttt) cc_final: 0.8389 (mtmp) REVERT: A 237 HIS cc_start: 0.7742 (t-90) cc_final: 0.7140 (m170) REVERT: A 242 LYS cc_start: 0.7577 (mmtm) cc_final: 0.7235 (tptm) REVERT: A 303 ARG cc_start: 0.7268 (ttp80) cc_final: 0.7024 (mtp85) REVERT: A 321 LYS cc_start: 0.7258 (mmtt) cc_final: 0.6988 (mmtm) REVERT: B 195 ASP cc_start: 0.8108 (p0) cc_final: 0.7899 (p0) REVERT: B 199 LYS cc_start: 0.8807 (mttt) cc_final: 0.8576 (mtmp) REVERT: B 237 HIS cc_start: 0.7782 (t-90) cc_final: 0.7381 (m170) REVERT: B 242 LYS cc_start: 0.7785 (mmtm) cc_final: 0.7511 (tptm) REVERT: B 321 LYS cc_start: 0.7485 (mmtt) cc_final: 0.7242 (mmtm) REVERT: C 199 LYS cc_start: 0.8908 (mttp) cc_final: 0.8691 (mtmp) REVERT: C 237 HIS cc_start: 0.7909 (t-90) cc_final: 0.7587 (m170) REVERT: C 242 LYS cc_start: 0.7984 (mmtm) cc_final: 0.7743 (tptm) REVERT: C 303 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7387 (mtp85) REVERT: C 321 LYS cc_start: 0.7507 (mmtt) cc_final: 0.7209 (mmtm) REVERT: D 195 ASP cc_start: 0.8146 (p0) cc_final: 0.7943 (p0) REVERT: D 199 LYS cc_start: 0.8788 (mttt) cc_final: 0.8542 (mtmp) REVERT: D 237 HIS cc_start: 0.7808 (t-90) cc_final: 0.7263 (m170) REVERT: D 242 LYS cc_start: 0.7845 (mmtm) cc_final: 0.7514 (tptm) REVERT: D 321 LYS cc_start: 0.7494 (mmtt) cc_final: 0.7255 (mmtm) outliers start: 6 outliers final: 4 residues processed: 143 average time/residue: 0.9991 time to fit residues: 150.6450 Evaluate side-chains 92 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 287 ASN D 282 ASN D 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.165252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.134369 restraints weight = 8131.219| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 0.74 r_work: 0.3251 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.129 Angle : 0.531 5.353 14464 Z= 0.287 Chirality : 0.042 0.161 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.557 56.970 1480 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.26 % Allowed : 5.13 % Favored : 93.62 % 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: 2.32 (0.19), residues: 712 sheet: -1.05 (0.35), residues: 224 loop : 0.68 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 257 TYR 0.019 0.002 TYR A 213 PHE 0.020 0.002 PHE B 144 TRP 0.014 0.002 TRP A 147 HIS 0.004 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00260 (10672) covalent geometry : angle 0.53114 (14464) hydrogen bonds : bond 0.05539 ( 596) hydrogen bonds : angle 4.75552 ( 1722) *********************** 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 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.514 Fit side-chains REVERT: A 199 LYS cc_start: 0.8835 (mttt) cc_final: 0.8588 (mtmp) REVERT: A 237 HIS cc_start: 0.7875 (t-90) cc_final: 0.7595 (m170) REVERT: A 242 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7508 (tptm) REVERT: A 311 LYS cc_start: 0.7798 (ttmt) cc_final: 0.7512 (tttp) REVERT: B 199 LYS cc_start: 0.8848 (mttt) cc_final: 0.8611 (mtmp) REVERT: B 237 HIS cc_start: 0.7862 (t-90) cc_final: 0.7660 (m170) REVERT: B 242 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7583 (tptm) REVERT: B 311 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7506 (tttp) REVERT: C 107 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8782 (ttmm) REVERT: C 199 LYS cc_start: 0.8837 (mttp) cc_final: 0.8598 (mtmp) REVERT: C 242 LYS cc_start: 0.7908 (mmtm) cc_final: 0.7608 (tptm) REVERT: C 321 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7508 (mmtm) REVERT: D 199 LYS cc_start: 0.8830 (mttt) cc_final: 0.8603 (mtmp) REVERT: D 237 HIS cc_start: 0.7858 (t-90) cc_final: 0.7542 (m170) REVERT: D 242 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7572 (tptm) REVERT: D 311 LYS cc_start: 0.7799 (ttmt) cc_final: 0.7515 (tttp) REVERT: D 321 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7702 (mmtm) outliers start: 14 outliers final: 5 residues processed: 99 average time/residue: 0.9705 time to fit residues: 101.6134 Evaluate side-chains 93 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 107 LYS Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP 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 134 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN D 136 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.165591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.133920 restraints weight = 8211.708| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 0.77 r_work: 0.3251 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10672 Z= 0.114 Angle : 0.496 5.563 14464 Z= 0.265 Chirality : 0.041 0.148 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.438 56.303 1480 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.17 % Allowed : 5.94 % Favored : 92.90 % 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: 2.07 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 736 sheet: -0.88 (0.37), residues: 204 loop : 0.55 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 330 TYR 0.018 0.002 TYR C 213 PHE 0.018 0.002 PHE C 144 TRP 0.010 0.002 TRP A 147 HIS 0.003 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00225 (10672) covalent geometry : angle 0.49613 (14464) hydrogen bonds : bond 0.05176 ( 596) hydrogen bonds : angle 4.56443 ( 1722) *********************** 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 103 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.418 Fit side-chains REVERT: A 199 LYS cc_start: 0.8832 (mttt) cc_final: 0.8588 (mtmp) REVERT: A 237 HIS cc_start: 0.7881 (t-90) cc_final: 0.7619 (m170) REVERT: A 242 LYS cc_start: 0.7819 (mmtm) cc_final: 0.7548 (tptm) REVERT: A 311 LYS cc_start: 0.7818 (ttmt) cc_final: 0.7549 (tttp) REVERT: B 173 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.7779 (t80) REVERT: B 199 LYS cc_start: 0.8847 (mttt) cc_final: 0.8606 (mtmp) REVERT: B 242 LYS cc_start: 0.7836 (mmtm) cc_final: 0.7601 (tptm) REVERT: B 311 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7533 (tttp) REVERT: C 67 ASP cc_start: 0.7191 (m-30) cc_final: 0.6955 (m-30) REVERT: C 107 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8791 (ttmm) REVERT: C 173 TYR cc_start: 0.9175 (OUTLIER) cc_final: 0.7794 (t80) REVERT: C 199 LYS cc_start: 0.8815 (mttp) cc_final: 0.8581 (mtmp) REVERT: C 242 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7627 (tptm) REVERT: C 321 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7554 (mmtm) REVERT: D 173 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.7797 (t80) REVERT: D 199 LYS cc_start: 0.8850 (mttt) cc_final: 0.8623 (mtmp) REVERT: D 237 HIS cc_start: 0.7873 (t-90) cc_final: 0.7620 (m170) REVERT: D 242 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7547 (tptm) REVERT: D 311 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7534 (tttp) outliers start: 13 outliers final: 4 residues processed: 103 average time/residue: 0.9311 time to fit residues: 101.7899 Evaluate side-chains 95 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 295 TRP 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 65 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 125 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 GLN C 168 ASN C 237 HIS D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.160783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129279 restraints weight = 8079.149| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 0.75 r_work: 0.3192 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.159 Angle : 0.578 6.412 14464 Z= 0.312 Chirality : 0.044 0.154 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.753 55.844 1480 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.08 % Allowed : 6.21 % Favored : 92.72 % 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: 1.90 (0.23), residues: 1364 helix: 2.42 (0.19), residues: 712 sheet: -1.09 (0.40), residues: 176 loop : 0.52 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 330 TYR 0.027 0.003 TYR D 213 PHE 0.020 0.002 PHE B 144 TRP 0.012 0.002 TRP A 147 HIS 0.003 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00325 (10672) covalent geometry : angle 0.57818 (14464) hydrogen bonds : bond 0.06571 ( 596) hydrogen bonds : angle 4.83621 ( 1722) *********************** 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 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.440 Fit side-chains REVERT: A 173 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8002 (t80) REVERT: A 199 LYS cc_start: 0.8884 (mttt) cc_final: 0.8635 (mtmp) REVERT: A 237 HIS cc_start: 0.7839 (t-90) cc_final: 0.7558 (m170) REVERT: A 242 LYS cc_start: 0.7857 (mmtm) cc_final: 0.7570 (tptm) REVERT: A 311 LYS cc_start: 0.7847 (ttmt) cc_final: 0.7568 (tttp) REVERT: B 67 ASP cc_start: 0.7212 (m-30) cc_final: 0.6994 (m-30) REVERT: B 173 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.7985 (t80) REVERT: B 199 LYS cc_start: 0.8881 (mttt) cc_final: 0.8627 (mtmp) REVERT: B 242 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7618 (tptm) REVERT: B 311 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7560 (tttp) REVERT: C 67 ASP cc_start: 0.7247 (m-30) cc_final: 0.7026 (m-30) REVERT: C 107 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8758 (ttmm) REVERT: C 173 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 199 LYS cc_start: 0.8876 (mttp) cc_final: 0.8631 (mtmp) REVERT: C 242 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7639 (tptm) REVERT: D 67 ASP cc_start: 0.7232 (m-30) cc_final: 0.7006 (m-30) REVERT: D 173 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8001 (t80) REVERT: D 199 LYS cc_start: 0.8892 (mttt) cc_final: 0.8649 (mtmp) REVERT: D 237 HIS cc_start: 0.7845 (t-90) cc_final: 0.7573 (m170) REVERT: D 242 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7586 (tptm) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 0.9085 time to fit residues: 103.0602 Evaluate side-chains 102 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP 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 66 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS B 241 GLN C 237 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.162927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.131441 restraints weight = 8133.260| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 0.77 r_work: 0.3214 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.125 Angle : 0.520 6.059 14464 Z= 0.279 Chirality : 0.042 0.149 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.572 55.829 1480 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.17 % Allowed : 6.29 % Favored : 92.54 % 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: 1.98 (0.23), residues: 1364 helix: 2.47 (0.19), residues: 740 sheet: -0.81 (0.37), residues: 204 loop : 0.44 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 330 TYR 0.022 0.002 TYR A 213 PHE 0.018 0.002 PHE C 144 TRP 0.008 0.002 TRP A 147 HIS 0.002 0.001 HIS D 196 Details of bonding type rmsd covalent geometry : bond 0.00251 (10672) covalent geometry : angle 0.52002 (14464) hydrogen bonds : bond 0.05576 ( 596) hydrogen bonds : angle 4.63682 ( 1722) *********************** 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 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.488 Fit side-chains REVERT: A 173 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 199 LYS cc_start: 0.8878 (mttt) cc_final: 0.8637 (mtmp) REVERT: A 237 HIS cc_start: 0.7863 (t-90) cc_final: 0.7601 (m170) REVERT: A 242 LYS cc_start: 0.7827 (mmtm) cc_final: 0.7550 (tptm) REVERT: A 311 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7542 (tttp) REVERT: B 67 ASP cc_start: 0.7199 (m-30) cc_final: 0.6982 (m-30) REVERT: B 173 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.7880 (t80) REVERT: B 199 LYS cc_start: 0.8889 (mttt) cc_final: 0.8640 (mtmp) REVERT: B 242 LYS cc_start: 0.7865 (mmtm) cc_final: 0.7598 (tptm) REVERT: B 311 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7547 (tttp) REVERT: C 67 ASP cc_start: 0.7204 (m-30) cc_final: 0.6985 (m-30) REVERT: C 107 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8747 (ttmm) REVERT: C 173 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.7895 (t80) REVERT: C 199 LYS cc_start: 0.8856 (mttp) cc_final: 0.8613 (mtmp) REVERT: C 242 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7640 (tptm) REVERT: D 67 ASP cc_start: 0.7188 (m-30) cc_final: 0.6973 (m-30) REVERT: D 173 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.7892 (t80) REVERT: D 199 LYS cc_start: 0.8894 (mttt) cc_final: 0.8661 (mtmp) REVERT: D 237 HIS cc_start: 0.7875 (t-90) cc_final: 0.7610 (m170) REVERT: D 242 LYS cc_start: 0.7905 (mmtm) cc_final: 0.7557 (tptm) REVERT: D 311 LYS cc_start: 0.7823 (ttmt) cc_final: 0.7551 (tttp) outliers start: 13 outliers final: 6 residues processed: 102 average time/residue: 0.9691 time to fit residues: 104.5058 Evaluate side-chains 104 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 TYR 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 88 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS B 241 GLN C 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.130440 restraints weight = 8114.230| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 0.77 r_work: 0.3211 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.128 Angle : 0.524 6.058 14464 Z= 0.281 Chirality : 0.042 0.149 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.572 55.653 1480 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.35 % Allowed : 5.67 % Favored : 92.99 % 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: 2.01 (0.23), residues: 1364 helix: 2.52 (0.19), residues: 736 sheet: -0.80 (0.37), residues: 204 loop : 0.40 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 330 TYR 0.023 0.002 TYR B 213 PHE 0.018 0.002 PHE C 144 TRP 0.008 0.002 TRP A 147 HIS 0.002 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00257 (10672) covalent geometry : angle 0.52353 (14464) hydrogen bonds : bond 0.05662 ( 596) hydrogen bonds : angle 4.63501 ( 1722) *********************** 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 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.484 Fit side-chains REVERT: A 173 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.7905 (t80) REVERT: A 199 LYS cc_start: 0.8875 (mttt) cc_final: 0.8638 (mtmp) REVERT: A 237 HIS cc_start: 0.7858 (t-90) cc_final: 0.7596 (m170) REVERT: A 242 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7557 (tptm) REVERT: B 67 ASP cc_start: 0.7200 (m-30) cc_final: 0.6985 (m-30) REVERT: B 107 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8749 (ttmm) REVERT: B 173 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.7990 (t80) REVERT: B 199 LYS cc_start: 0.8884 (mttt) cc_final: 0.8637 (mtmp) REVERT: B 242 LYS cc_start: 0.7885 (mmtm) cc_final: 0.7617 (tptm) REVERT: B 321 LYS cc_start: 0.7942 (mptp) cc_final: 0.7704 (mptt) REVERT: C 107 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8763 (ttmm) REVERT: C 173 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.7897 (t80) REVERT: C 199 LYS cc_start: 0.8881 (mttp) cc_final: 0.8640 (mtmp) REVERT: C 242 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7647 (tptm) REVERT: D 67 ASP cc_start: 0.7174 (m-30) cc_final: 0.6964 (m-30) REVERT: D 173 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.7894 (t80) REVERT: D 199 LYS cc_start: 0.8885 (mttt) cc_final: 0.8655 (mtmp) REVERT: D 237 HIS cc_start: 0.7877 (t-90) cc_final: 0.7607 (m170) REVERT: D 242 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7580 (tptm) REVERT: D 311 LYS cc_start: 0.7814 (ttmt) cc_final: 0.7538 (tttp) REVERT: D 321 LYS cc_start: 0.7999 (mptp) cc_final: 0.7744 (mptt) outliers start: 15 outliers final: 6 residues processed: 108 average time/residue: 0.9701 time to fit residues: 110.6904 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 TYR 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 79 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS B 241 GLN C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.162980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131356 restraints weight = 8094.931| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.76 r_work: 0.3224 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10672 Z= 0.124 Angle : 0.516 5.994 14464 Z= 0.277 Chirality : 0.042 0.150 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.530 55.631 1480 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.26 % Allowed : 5.94 % Favored : 92.81 % 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: 2.03 (0.23), residues: 1364 helix: 2.54 (0.19), residues: 740 sheet: -0.79 (0.37), residues: 204 loop : 0.38 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 68 TYR 0.022 0.002 TYR B 213 PHE 0.018 0.002 PHE C 144 TRP 0.008 0.002 TRP A 147 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00249 (10672) covalent geometry : angle 0.51589 (14464) hydrogen bonds : bond 0.05491 ( 596) hydrogen bonds : angle 4.59652 ( 1722) *********************** 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 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.460 Fit side-chains REVERT: A 173 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.7921 (t80) REVERT: A 199 LYS cc_start: 0.8844 (mttt) cc_final: 0.8597 (mtmp) REVERT: A 237 HIS cc_start: 0.7828 (t-90) cc_final: 0.7564 (m170) REVERT: A 242 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7531 (tptm) REVERT: B 67 ASP cc_start: 0.7131 (m-30) cc_final: 0.6901 (m-30) REVERT: B 107 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8732 (ttmm) REVERT: B 173 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.7889 (t80) REVERT: B 199 LYS cc_start: 0.8849 (mttt) cc_final: 0.8593 (mtmp) REVERT: B 242 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7588 (tptm) REVERT: B 311 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7489 (tttp) REVERT: B 321 LYS cc_start: 0.7920 (mptp) cc_final: 0.7664 (mptt) REVERT: C 107 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8733 (ttmm) REVERT: C 173 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.7910 (t80) REVERT: C 199 LYS cc_start: 0.8844 (mttp) cc_final: 0.8595 (mtmp) REVERT: C 242 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7611 (tptm) REVERT: D 67 ASP cc_start: 0.7149 (m-30) cc_final: 0.6936 (m-30) REVERT: D 173 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.7908 (t80) REVERT: D 199 LYS cc_start: 0.8851 (mttt) cc_final: 0.8610 (mtmp) REVERT: D 237 HIS cc_start: 0.7832 (t-90) cc_final: 0.7558 (m170) REVERT: D 242 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7553 (tptm) REVERT: D 311 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7492 (tttp) REVERT: D 321 LYS cc_start: 0.7940 (mptp) cc_final: 0.7691 (mptt) outliers start: 14 outliers final: 6 residues processed: 106 average time/residue: 0.9591 time to fit residues: 107.6428 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 TYR 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 56 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 ASN B 237 HIS C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.163691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132007 restraints weight = 8141.992| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 0.80 r_work: 0.3233 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10672 Z= 0.118 Angle : 0.504 5.933 14464 Z= 0.270 Chirality : 0.041 0.148 1644 Planarity : 0.003 0.031 1880 Dihedral : 5.472 55.712 1480 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.99 % Allowed : 6.03 % Favored : 92.99 % 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: 2.10 (0.23), residues: 1364 helix: 2.64 (0.19), residues: 736 sheet: -0.77 (0.37), residues: 204 loop : 0.38 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.021 0.002 TYR B 213 PHE 0.017 0.002 PHE A 144 TRP 0.007 0.001 TRP A 147 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00236 (10672) covalent geometry : angle 0.50386 (14464) hydrogen bonds : bond 0.05260 ( 596) hydrogen bonds : angle 4.53960 ( 1722) *********************** 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 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.418 Fit side-chains REVERT: A 173 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.7813 (t80) REVERT: A 199 LYS cc_start: 0.8851 (mttt) cc_final: 0.8611 (mtmp) REVERT: A 237 HIS cc_start: 0.7848 (t-90) cc_final: 0.7578 (m170) REVERT: A 242 LYS cc_start: 0.7818 (mmtm) cc_final: 0.7527 (tptm) REVERT: A 311 LYS cc_start: 0.7767 (ttmt) cc_final: 0.7495 (tttp) REVERT: B 67 ASP cc_start: 0.7128 (m-30) cc_final: 0.6913 (m-30) REVERT: B 173 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.7884 (t80) REVERT: B 199 LYS cc_start: 0.8860 (mttt) cc_final: 0.8608 (mtmp) REVERT: B 242 LYS cc_start: 0.7841 (mmtm) cc_final: 0.7576 (tptm) REVERT: B 311 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7495 (tttp) REVERT: B 321 LYS cc_start: 0.7921 (mptp) cc_final: 0.7675 (mptt) REVERT: C 107 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8741 (ttmm) REVERT: C 173 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.7910 (t80) REVERT: C 199 LYS cc_start: 0.8853 (mttp) cc_final: 0.8609 (mtmp) REVERT: C 242 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7614 (tptm) REVERT: D 67 ASP cc_start: 0.7141 (m-30) cc_final: 0.6922 (m-30) REVERT: D 173 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.7908 (t80) REVERT: D 199 LYS cc_start: 0.8861 (mttt) cc_final: 0.8626 (mtmp) REVERT: D 237 HIS cc_start: 0.7844 (t-90) cc_final: 0.7558 (m170) REVERT: D 242 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7552 (tptm) REVERT: D 311 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7495 (tttp) REVERT: D 321 LYS cc_start: 0.7926 (mptp) cc_final: 0.7690 (mptt) outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 0.9200 time to fit residues: 100.6329 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 139 LYS 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 128 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS C 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.162936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.131348 restraints weight = 8063.851| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.77 r_work: 0.3200 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10672 Z= 0.123 Angle : 0.515 5.957 14464 Z= 0.276 Chirality : 0.041 0.149 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.519 56.188 1480 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.17 % Allowed : 5.67 % Favored : 93.17 % 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: 2.02 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 740 sheet: -0.79 (0.36), residues: 204 loop : 0.35 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 258 TYR 0.023 0.002 TYR B 213 PHE 0.017 0.002 PHE C 144 TRP 0.008 0.002 TRP A 147 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00248 (10672) covalent geometry : angle 0.51515 (14464) hydrogen bonds : bond 0.05504 ( 596) hydrogen bonds : angle 4.58943 ( 1722) *********************** 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 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.586 Fit side-chains REVERT: A 173 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.7906 (t80) REVERT: A 199 LYS cc_start: 0.8899 (mttt) cc_final: 0.8669 (mtmp) REVERT: A 237 HIS cc_start: 0.7892 (t-90) cc_final: 0.7621 (m170) REVERT: A 242 LYS cc_start: 0.7844 (mmtm) cc_final: 0.7557 (tptm) REVERT: B 67 ASP cc_start: 0.7173 (m-30) cc_final: 0.6956 (m-30) REVERT: B 107 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8748 (ttmm) REVERT: B 173 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.7989 (t80) REVERT: B 199 LYS cc_start: 0.8898 (mttt) cc_final: 0.8658 (mtmp) REVERT: B 242 LYS cc_start: 0.7881 (mmtm) cc_final: 0.7617 (tptm) REVERT: B 311 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7552 (tttp) REVERT: B 321 LYS cc_start: 0.7950 (mptp) cc_final: 0.7725 (mptt) REVERT: C 107 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8764 (ttmm) REVERT: C 173 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.7899 (t80) REVERT: C 199 LYS cc_start: 0.8898 (mttp) cc_final: 0.8664 (mtmp) REVERT: C 242 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7652 (tptm) REVERT: D 67 ASP cc_start: 0.7192 (m-30) cc_final: 0.6967 (m-30) REVERT: D 107 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8799 (ttmm) REVERT: D 173 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.7893 (t80) REVERT: D 199 LYS cc_start: 0.8902 (mttt) cc_final: 0.8676 (mtmp) REVERT: D 237 HIS cc_start: 0.7883 (t-90) cc_final: 0.7595 (m170) REVERT: D 242 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7586 (tptm) REVERT: D 321 LYS cc_start: 0.7973 (mptp) cc_final: 0.7751 (mptt) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 0.9353 time to fit residues: 107.0779 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 TYR 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 15 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS C 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129833 restraints weight = 8068.927| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 0.75 r_work: 0.3190 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10672 Z= 0.134 Angle : 0.540 6.119 14464 Z= 0.290 Chirality : 0.042 0.148 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.606 55.959 1480 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.17 % Allowed : 5.94 % Favored : 92.90 % 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: 1.93 (0.23), residues: 1364 helix: 2.46 (0.19), residues: 736 sheet: -0.81 (0.37), residues: 204 loop : 0.35 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 258 TYR 0.025 0.002 TYR B 213 PHE 0.018 0.002 PHE C 144 TRP 0.009 0.002 TRP A 147 HIS 0.002 0.001 HIS C 20 Details of bonding type rmsd covalent geometry : bond 0.00273 (10672) covalent geometry : angle 0.53973 (14464) hydrogen bonds : bond 0.05889 ( 596) hydrogen bonds : angle 4.67733 ( 1722) ********************** 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 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.495 Fit side-chains REVERT: A 173 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.7894 (t80) REVERT: A 199 LYS cc_start: 0.8910 (mttt) cc_final: 0.8678 (mtmp) REVERT: A 237 HIS cc_start: 0.7892 (t-90) cc_final: 0.7616 (m170) REVERT: A 242 LYS cc_start: 0.7846 (mmtm) cc_final: 0.7565 (tptm) REVERT: B 67 ASP cc_start: 0.7159 (m-30) cc_final: 0.6941 (m-30) REVERT: B 107 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8756 (ttmm) REVERT: B 173 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.7979 (t80) REVERT: B 199 LYS cc_start: 0.8905 (mttt) cc_final: 0.8665 (mtmp) REVERT: B 242 LYS cc_start: 0.7888 (mmtm) cc_final: 0.7623 (tptm) REVERT: B 321 LYS cc_start: 0.7978 (mptp) cc_final: 0.7732 (mptt) REVERT: C 107 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8769 (ttmm) REVERT: C 173 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8000 (t80) REVERT: C 199 LYS cc_start: 0.8907 (mttp) cc_final: 0.8671 (mtmp) REVERT: C 242 LYS cc_start: 0.7974 (mmtm) cc_final: 0.7666 (tptm) REVERT: D 67 ASP cc_start: 0.7227 (m-30) cc_final: 0.7014 (m-30) REVERT: D 107 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8775 (ttmm) REVERT: D 173 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.7999 (t80) REVERT: D 199 LYS cc_start: 0.8914 (mttt) cc_final: 0.8686 (mtmp) REVERT: D 237 HIS cc_start: 0.7882 (t-90) cc_final: 0.7588 (m170) REVERT: D 242 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7600 (tptm) REVERT: D 321 LYS cc_start: 0.8004 (mptp) cc_final: 0.7763 (mptt) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 0.9009 time to fit residues: 103.0500 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 173 TYR 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 86 optimal weight: 0.0570 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 HIS C 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.162303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126891 restraints weight = 8059.550| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 0.79 r_work: 0.3231 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work: 0.2891 rms_B_bonded: 4.96 restraints_weight: 0.1250 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.129 Angle : 0.530 6.060 14464 Z= 0.284 Chirality : 0.042 0.147 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.567 55.980 1480 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.17 % Allowed : 5.67 % Favored : 93.17 % 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: 2.48 (0.19), residues: 740 sheet: -0.80 (0.37), residues: 204 loop : 0.34 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 200 TYR 0.023 0.002 TYR B 213 PHE 0.018 0.002 PHE C 144 TRP 0.008 0.002 TRP A 147 HIS 0.002 0.001 HIS B 20 Details of bonding type rmsd covalent geometry : bond 0.00262 (10672) covalent geometry : angle 0.52980 (14464) hydrogen bonds : bond 0.05681 ( 596) hydrogen bonds : angle 4.63110 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5446.61 seconds wall clock time: 93 minutes 40.60 seconds (5620.60 seconds total)