Starting phenix.real_space_refine on Sun May 3 08:37:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ob_75878/05_2026/11ob_75878.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ob_75878/05_2026/11ob_75878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11ob_75878/05_2026/11ob_75878.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ob_75878/05_2026/11ob_75878.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11ob_75878/05_2026/11ob_75878.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ob_75878/05_2026/11ob_75878.map" } resolution = 2.38 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= 0.008 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 3233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 11725 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: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 310 Classifications: {'water': 310} Link IDs: {None: 309} Chain: "B" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 294 Classifications: {'water': 294} Link IDs: {None: 293} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 325 Classifications: {'water': 325} Link IDs: {None: 324} Chain: "D" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 324 Classifications: {'water': 324} Link IDs: {None: 323} Time building chain proxies: 3.37, per 1000 atoms: 0.29 Number of scatterers: 11725 At special positions: 0 Unit cell: (100.695, 80.85, 108.78, 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 3233 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: 0.95 Conformation dependent library (CDL) restraints added in 524.7 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: 59 helices and 8 sheets defined 54.0% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.942A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.080A 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: 3.766A 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 258 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 6.408A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.178A 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: 3.789A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.777A 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: 3.628A 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: 6.523A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 5.177A 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: 3.737A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.032A 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 81 through 85 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 removed outlier: 3.533A pdb=" N ASN C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) 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 258 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 302 through 314 removed outlier: 6.357A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.275A 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: 3.858A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.066A 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: 3.861A 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 139 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 removed outlier: 3.515A pdb=" N GLY D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) 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: 5.705A pdb=" N GLY A 28 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 145 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLU A 187 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 6.219A 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: 6.702A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 187 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.214A 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: 5.772A pdb=" N GLY C 28 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 75 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL C 104 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA C 145 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE C 106 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TRP C 147 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 187 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.234A 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: 6.519A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.182A 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: 2.06 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2065 1.33 - 1.45: 2345 1.45 - 1.57: 6206 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" CA PRO D 261 " pdb=" C PRO D 261 " ideal model delta sigma weight residual 1.517 1.539 -0.022 6.70e-03 2.23e+04 1.04e+01 bond pdb=" N LYS B 293 " pdb=" CA LYS B 293 " ideal model delta sigma weight residual 1.462 1.492 -0.030 1.00e-02 1.00e+04 9.03e+00 bond pdb=" N VAL D 260 " pdb=" CA VAL D 260 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.57e+00 bond pdb=" N ILE D 77 " pdb=" CA ILE D 77 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.10e+00 bond pdb=" N VAL C 186 " pdb=" CA VAL C 186 " ideal model delta sigma weight residual 1.460 1.491 -0.031 1.10e-02 8.26e+03 8.08e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 13716 1.67 - 3.33: 654 3.33 - 5.00: 74 5.00 - 6.66: 17 6.66 - 8.33: 3 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 113.80 118.68 -4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" CA PHE A 144 " pdb=" CB PHE A 144 " pdb=" CG PHE A 144 " ideal model delta sigma weight residual 113.80 118.46 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C HIS D 4 " pdb=" CA HIS D 4 " pdb=" CB HIS D 4 " ideal model delta sigma weight residual 110.17 114.91 -4.74 1.11e+00 8.12e-01 1.82e+01 angle pdb=" CA PRO D 188 " pdb=" N PRO D 188 " pdb=" CD PRO D 188 " ideal model delta sigma weight residual 112.00 106.03 5.97 1.40e+00 5.10e-01 1.82e+01 angle pdb=" CA PRO A 188 " pdb=" N PRO A 188 " pdb=" CD PRO A 188 " ideal model delta sigma weight residual 112.00 106.33 5.67 1.40e+00 5.10e-01 1.64e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6047 17.98 - 35.97: 348 35.97 - 53.95: 77 53.95 - 71.94: 20 71.94 - 89.92: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: 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 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CG ARG C 133 " pdb=" CD ARG C 133 " pdb=" NE ARG C 133 " pdb=" CZ ARG C 133 " ideal model delta sinusoidal sigma weight residual -180.00 -135.19 -44.81 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG C 172 " pdb=" CD ARG C 172 " pdb=" NE ARG C 172 " pdb=" CZ ARG C 172 " ideal model delta sinusoidal sigma weight residual 90.00 133.80 -43.80 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1204 0.046 - 0.092: 292 0.092 - 0.138: 113 0.138 - 0.185: 29 0.185 - 0.231: 6 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA LYS A 329 " pdb=" N LYS A 329 " pdb=" C LYS A 329 " pdb=" CB LYS A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LEU D 61 " pdb=" N LEU D 61 " pdb=" C LEU D 61 " pdb=" CB LEU D 61 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ARG D 172 " pdb=" N ARG D 172 " pdb=" C ARG D 172 " pdb=" CB ARG D 172 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 60 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C GLN D 60 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN D 60 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU D 61 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 292 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C LEU B 292 " 0.041 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 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C THR D 259 " 0.035 2.00e-02 2.50e+03 pdb=" O THR D 259 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL D 260 " -0.012 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3276 2.80 - 3.33: 11794 3.33 - 3.85: 22935 3.85 - 4.38: 27896 4.38 - 4.90: 43044 Nonbonded interactions: 108945 Sorted by model distance: nonbonded pdb=" O GLN C 60 " pdb=" OG1 THR C 64 " model vdw 2.279 3.040 nonbonded pdb=" OE1 GLU D 155 " pdb=" O HOH D 401 " model vdw 2.301 3.040 nonbonded pdb=" OE2 GLU A 246 " pdb=" O HOH A 401 " model vdw 2.302 3.040 nonbonded pdb=" O ALA A 32 " pdb=" O HOH A 402 " model vdw 2.306 3.040 nonbonded pdb=" O HOH D 527 " pdb=" O HOH D 677 " model vdw 2.307 3.040 ... (remaining 108940 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.890 Find NCS groups from input model: 0.170 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:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.038 10672 Z= 0.340 Angle : 0.765 8.331 14464 Z= 0.512 Chirality : 0.051 0.231 1644 Planarity : 0.005 0.034 1880 Dihedral : 12.964 89.921 3984 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.90 % Allowed : 1.35 % Favored : 97.75 % 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: 0.74 (0.22), residues: 1364 helix: 1.37 (0.19), residues: 704 sheet: -1.67 (0.35), residues: 184 loop : 0.27 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.020 0.002 TYR D 213 PHE 0.026 0.002 PHE D 144 TRP 0.014 0.003 TRP B 313 HIS 0.005 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00485 (10672) covalent geometry : angle 0.76477 (14464) hydrogen bonds : bond 0.15210 ( 576) hydrogen bonds : angle 5.86135 ( 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 181 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.499 Fit side-chains REVERT: A 42 ARG cc_start: 0.6893 (mtp180) cc_final: 0.6672 (mmp80) REVERT: A 52 GLU cc_start: 0.7506 (tt0) cc_final: 0.7121 (tt0) REVERT: A 86 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7883 (mtpt) REVERT: A 152 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7987 (tttm) REVERT: A 199 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7749 (mmmt) REVERT: A 237 HIS cc_start: 0.7961 (t-170) cc_final: 0.7523 (m-70) REVERT: A 250 MET cc_start: 0.8614 (tpp) cc_final: 0.8410 (tpp) REVERT: A 311 LYS cc_start: 0.7689 (tttp) cc_final: 0.6785 (ttpt) REVERT: A 341 LYS cc_start: 0.8361 (mttm) cc_final: 0.8053 (mtmm) REVERT: B 2 HIS cc_start: 0.4687 (OUTLIER) cc_final: 0.4361 (t70) REVERT: B 13 LYS cc_start: 0.8626 (tttm) cc_final: 0.8261 (ttpt) REVERT: B 41 LYS cc_start: 0.7959 (mmtm) cc_final: 0.7638 (mttt) REVERT: B 49 GLU cc_start: 0.7574 (pm20) cc_final: 0.6738 (tp30) REVERT: B 303 ARG cc_start: 0.7619 (mtp85) cc_final: 0.6680 (mmp-170) REVERT: B 311 LYS cc_start: 0.7580 (mmtp) cc_final: 0.7306 (ttpt) REVERT: C 42 ARG cc_start: 0.6982 (mtp180) cc_final: 0.5871 (mmp80) REVERT: C 152 LYS cc_start: 0.7989 (tptp) cc_final: 0.7419 (ptpt) REVERT: C 199 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7820 (mmpt) REVERT: C 242 LYS cc_start: 0.7816 (mttt) cc_final: 0.7558 (mptt) REVERT: C 303 ARG cc_start: 0.6882 (mtp-110) cc_final: 0.6497 (mmm-85) REVERT: D 13 LYS cc_start: 0.8428 (tttp) cc_final: 0.7982 (ttpt) REVERT: D 193 ASP cc_start: 0.8482 (m-30) cc_final: 0.8234 (m-30) REVERT: D 199 LYS cc_start: 0.8399 (mttp) cc_final: 0.7446 (mptp) REVERT: D 242 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7383 (tppt) REVERT: D 303 ARG cc_start: 0.6822 (ttp80) cc_final: 0.6285 (ttt-90) REVERT: D 341 LYS cc_start: 0.7960 (mttm) cc_final: 0.7276 (mmpt) outliers start: 10 outliers final: 4 residues processed: 180 average time/residue: 0.9493 time to fit residues: 179.7317 Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 2 HIS 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: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 95 GLN B 166 ASN B 319 ASN C 70 ASN C 168 ASN C 241 GLN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114436 restraints weight = 11034.448| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.26 r_work: 0.3202 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10672 Z= 0.119 Angle : 0.519 8.290 14464 Z= 0.269 Chirality : 0.040 0.151 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.322 56.307 1482 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.26 % Allowed : 6.21 % 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: 1.49 (0.23), residues: 1364 helix: 2.20 (0.19), residues: 716 sheet: -1.72 (0.33), residues: 204 loop : 0.48 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 42 TYR 0.020 0.002 TYR D 213 PHE 0.017 0.001 PHE D 144 TRP 0.013 0.002 TRP D 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00260 (10672) covalent geometry : angle 0.51906 (14464) hydrogen bonds : bond 0.05022 ( 576) hydrogen bonds : angle 4.29462 ( 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 124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.394 Fit side-chains REVERT: A 42 ARG cc_start: 0.6932 (mtp180) cc_final: 0.6624 (mmp80) REVERT: A 52 GLU cc_start: 0.7420 (tt0) cc_final: 0.7043 (tt0) REVERT: A 53 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.6981 (tm-30) REVERT: A 86 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7832 (mtpt) REVERT: A 152 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7912 (tttm) REVERT: A 199 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7725 (mmmt) REVERT: A 237 HIS cc_start: 0.7923 (t-170) cc_final: 0.7469 (m-70) REVERT: A 250 MET cc_start: 0.8629 (tpp) cc_final: 0.8366 (tpp) REVERT: A 311 LYS cc_start: 0.7644 (tttp) cc_final: 0.6776 (ttpt) REVERT: A 341 LYS cc_start: 0.8348 (mttm) cc_final: 0.8040 (mtmm) REVERT: B 13 LYS cc_start: 0.8569 (tttm) cc_final: 0.8104 (ttpt) REVERT: B 41 LYS cc_start: 0.7781 (mmtm) cc_final: 0.7463 (mttt) REVERT: B 49 GLU cc_start: 0.7670 (pm20) cc_final: 0.6522 (tp30) REVERT: B 52 GLU cc_start: 0.7828 (tt0) cc_final: 0.7418 (tt0) REVERT: B 303 ARG cc_start: 0.7598 (mtp85) cc_final: 0.6953 (mmp-170) REVERT: B 311 LYS cc_start: 0.7467 (mmtp) cc_final: 0.7084 (ttpt) REVERT: C 42 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6019 (mmp80) REVERT: C 152 LYS cc_start: 0.7970 (tptp) cc_final: 0.7172 (ptpt) REVERT: C 199 LYS cc_start: 0.8362 (mtmt) cc_final: 0.7689 (mmpt) REVERT: C 242 LYS cc_start: 0.7780 (mttt) cc_final: 0.7520 (mptt) REVERT: C 303 ARG cc_start: 0.7047 (mtp-110) cc_final: 0.6303 (ttt-90) REVERT: D 13 LYS cc_start: 0.8417 (tttp) cc_final: 0.7927 (ttpt) REVERT: D 165 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: D 173 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8310 (t80) REVERT: D 199 LYS cc_start: 0.8388 (mttp) cc_final: 0.7570 (mmpt) REVERT: D 242 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7372 (tppt) REVERT: D 246 GLU cc_start: 0.8170 (mp0) cc_final: 0.7806 (mp0) REVERT: D 303 ARG cc_start: 0.6825 (ttp80) cc_final: 0.6430 (ttt-90) REVERT: D 341 LYS cc_start: 0.7982 (mttm) cc_final: 0.7214 (mmpt) outliers start: 14 outliers final: 5 residues processed: 121 average time/residue: 1.0153 time to fit residues: 129.1766 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU 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 C residue 343 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR 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 111 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN C 241 GLN C 319 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.141798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109885 restraints weight = 11158.814| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.25 r_work: 0.3139 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10672 Z= 0.147 Angle : 0.542 7.079 14464 Z= 0.284 Chirality : 0.042 0.150 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.336 56.353 1480 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.08 % Allowed : 7.37 % Favored : 91.55 % 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: 1.50 (0.23), residues: 1364 helix: 2.30 (0.19), residues: 716 sheet: -1.72 (0.34), residues: 204 loop : 0.33 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 330 TYR 0.026 0.002 TYR D 213 PHE 0.016 0.002 PHE C 144 TRP 0.018 0.002 TRP D 147 HIS 0.007 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00333 (10672) covalent geometry : angle 0.54230 (14464) hydrogen bonds : bond 0.05757 ( 576) hydrogen bonds : angle 4.20742 ( 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 119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.493 Fit side-chains REVERT: A 42 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6584 (mmp80) REVERT: A 52 GLU cc_start: 0.7444 (tt0) cc_final: 0.7058 (tt0) REVERT: A 86 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7826 (mtpt) REVERT: A 152 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7943 (tttm) REVERT: A 199 LYS cc_start: 0.8493 (mtmt) cc_final: 0.7798 (tptp) REVERT: A 237 HIS cc_start: 0.7981 (t-170) cc_final: 0.7464 (m-70) REVERT: A 250 MET cc_start: 0.8670 (tpp) cc_final: 0.8414 (tpp) REVERT: A 311 LYS cc_start: 0.7735 (tttp) cc_final: 0.6830 (ttpt) REVERT: A 341 LYS cc_start: 0.8411 (mttm) cc_final: 0.8066 (mtmm) REVERT: B 13 LYS cc_start: 0.8635 (tttm) cc_final: 0.8147 (ttpt) REVERT: B 41 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7423 (mttt) REVERT: B 49 GLU cc_start: 0.7767 (pm20) cc_final: 0.6704 (tp30) REVERT: B 52 GLU cc_start: 0.7903 (tt0) cc_final: 0.7539 (tt0) REVERT: B 303 ARG cc_start: 0.7726 (mtp85) cc_final: 0.7064 (mmp-170) REVERT: B 311 LYS cc_start: 0.7464 (mmtp) cc_final: 0.7103 (ttpt) REVERT: C 42 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6171 (mmp80) REVERT: C 152 LYS cc_start: 0.7987 (tptp) cc_final: 0.7142 (ptpt) REVERT: C 199 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7776 (mmpt) REVERT: C 242 LYS cc_start: 0.7879 (mttt) cc_final: 0.7557 (mptt) REVERT: C 303 ARG cc_start: 0.7035 (mtp-110) cc_final: 0.6374 (ttt-90) REVERT: D 13 LYS cc_start: 0.8464 (tttp) cc_final: 0.8223 (tttt) REVERT: D 165 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: D 199 LYS cc_start: 0.8456 (mttp) cc_final: 0.7650 (mmpt) REVERT: D 242 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7387 (tppt) REVERT: D 246 GLU cc_start: 0.8213 (mp0) cc_final: 0.7803 (mp0) REVERT: D 303 ARG cc_start: 0.6801 (ttp80) cc_final: 0.6258 (tmt-80) REVERT: D 341 LYS cc_start: 0.7998 (mttm) cc_final: 0.7240 (mmpt) outliers start: 12 outliers final: 8 residues processed: 116 average time/residue: 1.0437 time to fit residues: 127.3621 Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER 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 C residue 343 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 17 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN C 241 GLN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110828 restraints weight = 11176.930| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.26 r_work: 0.3154 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1573 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= 0.129 Angle : 0.506 6.086 14464 Z= 0.265 Chirality : 0.041 0.144 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.233 56.194 1480 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.44 % Allowed : 7.82 % Favored : 90.74 % 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: 1.63 (0.23), residues: 1364 helix: 2.46 (0.19), residues: 716 sheet: -1.73 (0.34), residues: 204 loop : 0.31 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.023 0.002 TYR D 213 PHE 0.016 0.002 PHE B 144 TRP 0.014 0.002 TRP D 147 HIS 0.005 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00294 (10672) covalent geometry : angle 0.50650 (14464) hydrogen bonds : bond 0.05193 ( 576) hydrogen bonds : angle 4.10054 ( 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 119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.526 Fit side-chains REVERT: A 42 ARG cc_start: 0.6920 (mtp180) cc_final: 0.6608 (mmp80) REVERT: A 52 GLU cc_start: 0.7403 (tt0) cc_final: 0.6971 (tt0) REVERT: A 86 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7818 (mtpt) REVERT: A 152 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7945 (tttm) REVERT: A 199 LYS cc_start: 0.8490 (mtmt) cc_final: 0.7795 (mmmt) REVERT: A 237 HIS cc_start: 0.7992 (t-170) cc_final: 0.7471 (m-70) REVERT: A 250 MET cc_start: 0.8651 (tpp) cc_final: 0.8421 (tpp) REVERT: A 311 LYS cc_start: 0.7680 (tttp) cc_final: 0.6790 (ttpt) REVERT: A 341 LYS cc_start: 0.8364 (mttm) cc_final: 0.8028 (mtmm) REVERT: B 13 LYS cc_start: 0.8609 (tttm) cc_final: 0.8111 (ttpt) REVERT: B 41 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7369 (mttt) REVERT: B 49 GLU cc_start: 0.7741 (pm20) cc_final: 0.6744 (tp30) REVERT: B 52 GLU cc_start: 0.7921 (tt0) cc_final: 0.7596 (tt0) REVERT: B 303 ARG cc_start: 0.7649 (mtp85) cc_final: 0.7009 (mmp-170) REVERT: B 311 LYS cc_start: 0.7496 (mmtp) cc_final: 0.7103 (ttpt) REVERT: C 42 ARG cc_start: 0.7318 (mtp180) cc_final: 0.6234 (mmp80) REVERT: C 152 LYS cc_start: 0.8002 (tptp) cc_final: 0.7147 (ptpt) REVERT: C 199 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7763 (mmpt) REVERT: C 242 LYS cc_start: 0.7901 (mttt) cc_final: 0.7548 (mptt) REVERT: C 303 ARG cc_start: 0.7003 (mtp-110) cc_final: 0.6369 (ttt-90) REVERT: D 13 LYS cc_start: 0.8417 (tttp) cc_final: 0.8191 (tmmt) REVERT: D 165 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7718 (mm-30) REVERT: D 199 LYS cc_start: 0.8423 (mttp) cc_final: 0.7622 (mmpt) REVERT: D 242 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7378 (tppt) REVERT: D 246 GLU cc_start: 0.8202 (mp0) cc_final: 0.7753 (mp0) REVERT: D 303 ARG cc_start: 0.6890 (ttp80) cc_final: 0.6444 (ttt-90) REVERT: D 341 LYS cc_start: 0.7989 (mttm) cc_final: 0.7220 (mmpt) outliers start: 16 outliers final: 10 residues processed: 117 average time/residue: 1.0280 time to fit residues: 126.6203 Evaluate side-chains 112 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 102 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 95 GLN C 241 GLN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112699 restraints weight = 11113.954| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.25 r_work: 0.3181 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1650 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= 0.107 Angle : 0.469 5.546 14464 Z= 0.244 Chirality : 0.040 0.134 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.074 56.263 1480 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.71 % Allowed : 7.91 % Favored : 90.38 % 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: 1.82 (0.23), residues: 1364 helix: 2.64 (0.19), residues: 716 sheet: -1.69 (0.34), residues: 204 loop : 0.37 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 303 TYR 0.020 0.001 TYR D 213 PHE 0.016 0.001 PHE B 144 TRP 0.011 0.001 TRP C 147 HIS 0.002 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00239 (10672) covalent geometry : angle 0.46874 (14464) hydrogen bonds : bond 0.04598 ( 576) hydrogen bonds : angle 3.97101 ( 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 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.478 Fit side-chains REVERT: A 42 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6650 (mmp80) REVERT: A 52 GLU cc_start: 0.7441 (tt0) cc_final: 0.7008 (tt0) REVERT: A 86 LYS cc_start: 0.8235 (mtmm) cc_final: 0.7842 (mtpt) REVERT: A 152 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7904 (tttm) REVERT: A 199 LYS cc_start: 0.8391 (mtmt) cc_final: 0.7692 (mmmt) REVERT: A 237 HIS cc_start: 0.7979 (t-170) cc_final: 0.7479 (m-70) REVERT: A 250 MET cc_start: 0.8664 (tpp) cc_final: 0.8391 (tpp) REVERT: A 311 LYS cc_start: 0.7613 (tttp) cc_final: 0.6731 (ttpt) REVERT: A 316 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7073 (ptpt) REVERT: A 341 LYS cc_start: 0.8366 (mttm) cc_final: 0.8016 (mtmm) REVERT: B 13 LYS cc_start: 0.8546 (tttm) cc_final: 0.8057 (ttpt) REVERT: B 41 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7374 (mttt) REVERT: B 49 GLU cc_start: 0.7728 (pm20) cc_final: 0.6782 (tp30) REVERT: B 52 GLU cc_start: 0.7894 (tt0) cc_final: 0.7582 (tt0) REVERT: B 303 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7018 (mmp-170) REVERT: B 311 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7044 (ttpt) REVERT: C 42 ARG cc_start: 0.7357 (mtp180) cc_final: 0.6283 (mmp80) REVERT: C 152 LYS cc_start: 0.7979 (tptp) cc_final: 0.7137 (ptpt) REVERT: C 199 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7741 (mmpt) REVERT: C 242 LYS cc_start: 0.7885 (mttt) cc_final: 0.7539 (mptt) REVERT: C 303 ARG cc_start: 0.6984 (mtp-110) cc_final: 0.6336 (ttt-90) REVERT: D 13 LYS cc_start: 0.8376 (tttp) cc_final: 0.8146 (tttt) REVERT: D 38 SER cc_start: 0.8163 (t) cc_final: 0.7735 (m) REVERT: D 165 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: D 199 LYS cc_start: 0.8377 (mttp) cc_final: 0.7353 (mptp) REVERT: D 242 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7416 (tppt) REVERT: D 303 ARG cc_start: 0.6869 (ttp80) cc_final: 0.6355 (tmt-80) REVERT: D 341 LYS cc_start: 0.7978 (mttm) cc_final: 0.7241 (mmpt) outliers start: 19 outliers final: 9 residues processed: 117 average time/residue: 0.9469 time to fit residues: 116.9067 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 65 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 95 GLN C 241 GLN D 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112913 restraints weight = 11068.563| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.26 r_work: 0.3184 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1710 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= 0.106 Angle : 0.466 6.619 14464 Z= 0.242 Chirality : 0.040 0.132 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.015 56.466 1480 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.53 % Allowed : 8.36 % Favored : 90.11 % 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: 1.87 (0.23), residues: 1364 helix: 2.69 (0.19), residues: 716 sheet: -1.70 (0.34), residues: 204 loop : 0.39 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.020 0.001 TYR D 213 PHE 0.015 0.001 PHE B 144 TRP 0.012 0.001 TRP D 147 HIS 0.003 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00238 (10672) covalent geometry : angle 0.46570 (14464) hydrogen bonds : bond 0.04526 ( 576) hydrogen bonds : angle 3.92920 ( 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 117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.456 Fit side-chains REVERT: A 42 ARG cc_start: 0.6928 (mtp180) cc_final: 0.6627 (mmp80) REVERT: A 52 GLU cc_start: 0.7434 (tt0) cc_final: 0.6988 (tt0) REVERT: A 86 LYS cc_start: 0.8273 (mtmm) cc_final: 0.7868 (mtpt) REVERT: A 152 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7905 (tttm) REVERT: A 199 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7674 (mmmt) REVERT: A 237 HIS cc_start: 0.7966 (t-170) cc_final: 0.7474 (m-70) REVERT: A 250 MET cc_start: 0.8658 (tpp) cc_final: 0.8394 (tpp) REVERT: A 311 LYS cc_start: 0.7597 (tttp) cc_final: 0.6666 (ttpt) REVERT: A 316 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7384 (ptpp) REVERT: A 341 LYS cc_start: 0.8306 (mttm) cc_final: 0.7968 (mtmm) REVERT: B 13 LYS cc_start: 0.8550 (tttm) cc_final: 0.8054 (ttpt) REVERT: B 41 LYS cc_start: 0.7909 (mmtm) cc_final: 0.7330 (mttt) REVERT: B 49 GLU cc_start: 0.7713 (pm20) cc_final: 0.6786 (tp30) REVERT: B 52 GLU cc_start: 0.7898 (tt0) cc_final: 0.7596 (tt0) REVERT: B 303 ARG cc_start: 0.7631 (mtp85) cc_final: 0.7033 (mmp-170) REVERT: B 311 LYS cc_start: 0.7425 (mmtp) cc_final: 0.7016 (ttpt) REVERT: C 42 ARG cc_start: 0.7356 (mtp180) cc_final: 0.6284 (mmp80) REVERT: C 152 LYS cc_start: 0.7982 (tptp) cc_final: 0.7132 (ptpt) REVERT: C 199 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7730 (mmpt) REVERT: C 242 LYS cc_start: 0.7892 (mttt) cc_final: 0.7527 (mptt) REVERT: C 303 ARG cc_start: 0.6936 (mtp-110) cc_final: 0.6298 (ttt-90) REVERT: D 13 LYS cc_start: 0.8396 (tttp) cc_final: 0.8141 (tttt) REVERT: D 165 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: D 199 LYS cc_start: 0.8373 (mttp) cc_final: 0.7346 (mptp) REVERT: D 242 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7349 (tppt) REVERT: D 303 ARG cc_start: 0.6892 (ttp80) cc_final: 0.6423 (ttt-90) REVERT: D 341 LYS cc_start: 0.7935 (mttm) cc_final: 0.7213 (mmpt) outliers start: 17 outliers final: 11 residues processed: 115 average time/residue: 0.9577 time to fit residues: 116.2846 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 : 0.452 ------------------------------------------------------------------------------- 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 343 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 131 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 95 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 = 0.3646 r_free = 0.3646 target = 0.142679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110794 restraints weight = 11075.130| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.26 r_work: 0.3153 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1716 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= 0.124 Angle : 0.495 6.590 14464 Z= 0.258 Chirality : 0.041 0.142 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.130 56.177 1480 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.35 % Allowed : 8.63 % Favored : 90.02 % 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: 1.78 (0.23), residues: 1364 helix: 2.61 (0.19), residues: 716 sheet: -1.73 (0.34), residues: 204 loop : 0.35 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 303 TYR 0.024 0.002 TYR D 213 PHE 0.016 0.002 PHE B 144 TRP 0.014 0.002 TRP D 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00280 (10672) covalent geometry : angle 0.49539 (14464) hydrogen bonds : bond 0.05077 ( 576) hydrogen bonds : angle 4.00112 ( 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 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.456 Fit side-chains REVERT: A 42 ARG cc_start: 0.6897 (mtp180) cc_final: 0.6623 (mmp80) REVERT: A 52 GLU cc_start: 0.7516 (tt0) cc_final: 0.7053 (tt0) REVERT: A 86 LYS cc_start: 0.8306 (mtmm) cc_final: 0.7871 (mtpt) REVERT: A 152 LYS cc_start: 0.8440 (ttmt) cc_final: 0.7890 (tttm) REVERT: A 199 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7720 (mmmt) REVERT: A 237 HIS cc_start: 0.7972 (t-170) cc_final: 0.7448 (m-70) REVERT: A 250 MET cc_start: 0.8673 (tpp) cc_final: 0.8427 (tpp) REVERT: A 311 LYS cc_start: 0.7662 (tttp) cc_final: 0.6730 (ttpt) REVERT: A 341 LYS cc_start: 0.8334 (mttm) cc_final: 0.8006 (mtmm) REVERT: B 13 LYS cc_start: 0.8614 (tttm) cc_final: 0.8122 (ttpt) REVERT: B 41 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7326 (mttt) REVERT: B 49 GLU cc_start: 0.7736 (pm20) cc_final: 0.6779 (tp30) REVERT: B 52 GLU cc_start: 0.7902 (tt0) cc_final: 0.7606 (tt0) REVERT: B 303 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7054 (mmp-170) REVERT: B 311 LYS cc_start: 0.7476 (mmtp) cc_final: 0.7058 (ttpt) REVERT: C 42 ARG cc_start: 0.7372 (mtp180) cc_final: 0.6347 (mmp80) REVERT: C 152 LYS cc_start: 0.8002 (tptp) cc_final: 0.7159 (ptpt) REVERT: C 199 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7761 (mmpt) REVERT: C 242 LYS cc_start: 0.7897 (mttt) cc_final: 0.7514 (mptt) REVERT: C 303 ARG cc_start: 0.6985 (mtp-110) cc_final: 0.6347 (ttt-90) REVERT: D 13 LYS cc_start: 0.8436 (tttp) cc_final: 0.8184 (tmmt) REVERT: D 165 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: D 199 LYS cc_start: 0.8409 (mttp) cc_final: 0.7609 (mmpt) REVERT: D 242 LYS cc_start: 0.7891 (mmtm) cc_final: 0.7353 (tppt) REVERT: D 303 ARG cc_start: 0.6920 (ttp80) cc_final: 0.6395 (ttt-90) REVERT: D 341 LYS cc_start: 0.7950 (mttm) cc_final: 0.7210 (mmpt) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 0.9285 time to fit residues: 107.8169 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 : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.0070 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 95 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 = 0.3659 r_free = 0.3659 target = 0.143828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111971 restraints weight = 11069.348| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.26 r_work: 0.3171 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1746 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= 0.113 Angle : 0.475 6.581 14464 Z= 0.247 Chirality : 0.040 0.136 1644 Planarity : 0.004 0.033 1880 Dihedral : 5.050 56.253 1480 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.44 % Allowed : 8.72 % 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: 2.67 (0.19), residues: 716 sheet: -1.71 (0.34), residues: 204 loop : 0.38 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.021 0.001 TYR D 213 PHE 0.016 0.001 PHE B 144 TRP 0.011 0.001 TRP D 147 HIS 0.003 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00255 (10672) covalent geometry : angle 0.47496 (14464) hydrogen bonds : bond 0.04706 ( 576) hydrogen bonds : angle 3.94768 ( 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 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.540 Fit side-chains REVERT: A 42 ARG cc_start: 0.6872 (mtp180) cc_final: 0.6584 (mmp80) REVERT: A 52 GLU cc_start: 0.7527 (tt0) cc_final: 0.7046 (tt0) REVERT: A 86 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7848 (mtpt) REVERT: A 152 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7887 (tttm) REVERT: A 199 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7689 (mmmt) REVERT: A 237 HIS cc_start: 0.7979 (t-170) cc_final: 0.7466 (m-70) REVERT: A 250 MET cc_start: 0.8664 (tpp) cc_final: 0.8415 (tpp) REVERT: A 311 LYS cc_start: 0.7618 (tttp) cc_final: 0.6678 (ttpt) REVERT: A 316 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7400 (ptpp) REVERT: A 341 LYS cc_start: 0.8315 (mttm) cc_final: 0.7994 (mtmm) REVERT: B 13 LYS cc_start: 0.8580 (tttm) cc_final: 0.8071 (ttpt) REVERT: B 41 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7331 (mttt) REVERT: B 49 GLU cc_start: 0.7719 (pm20) cc_final: 0.6757 (tp30) REVERT: B 52 GLU cc_start: 0.7890 (tt0) cc_final: 0.7593 (tt0) REVERT: B 303 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7037 (mmp-170) REVERT: B 311 LYS cc_start: 0.7455 (mmtp) cc_final: 0.7023 (ttpt) REVERT: C 42 ARG cc_start: 0.7373 (mtp180) cc_final: 0.6340 (mmp80) REVERT: C 152 LYS cc_start: 0.7987 (tptp) cc_final: 0.7133 (ptpt) REVERT: C 199 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7737 (mmpt) REVERT: C 242 LYS cc_start: 0.7897 (mttt) cc_final: 0.7509 (mptt) REVERT: C 303 ARG cc_start: 0.6959 (mtp-110) cc_final: 0.6318 (ttt-90) REVERT: D 13 LYS cc_start: 0.8411 (tttp) cc_final: 0.8146 (tttt) REVERT: D 165 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: D 199 LYS cc_start: 0.8383 (mttp) cc_final: 0.7577 (mmpt) REVERT: D 242 LYS cc_start: 0.7860 (mmtm) cc_final: 0.7346 (tppt) REVERT: D 303 ARG cc_start: 0.6908 (ttp80) cc_final: 0.6384 (ttt-90) REVERT: D 341 LYS cc_start: 0.7929 (mttm) cc_final: 0.7177 (mmpt) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.9869 time to fit residues: 112.4478 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 51 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 102 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 95 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 = 0.3603 r_free = 0.3603 target = 0.139961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107956 restraints weight = 10861.763| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.26 r_work: 0.3102 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1739 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= 0.133 Angle : 0.508 6.626 14464 Z= 0.265 Chirality : 0.041 0.145 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.176 55.970 1480 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.53 % Allowed : 8.54 % Favored : 89.93 % 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: 1.73 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 716 sheet: -1.74 (0.34), residues: 204 loop : 0.34 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.026 0.002 TYR D 213 PHE 0.016 0.002 PHE B 144 TRP 0.015 0.002 TRP D 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00304 (10672) covalent geometry : angle 0.50757 (14464) hydrogen bonds : bond 0.05297 ( 576) hydrogen bonds : angle 4.03508 ( 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: 17 poor density : 94 time to evaluate : 0.380 Fit side-chains REVERT: A 42 ARG cc_start: 0.6903 (mtp180) cc_final: 0.6628 (mmp80) REVERT: A 52 GLU cc_start: 0.7517 (tt0) cc_final: 0.7033 (tt0) REVERT: A 86 LYS cc_start: 0.8276 (mtmm) cc_final: 0.7834 (mtpt) REVERT: A 152 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7848 (tttm) REVERT: A 199 LYS cc_start: 0.8352 (mtmt) cc_final: 0.7674 (mmmt) REVERT: A 237 HIS cc_start: 0.7964 (t-170) cc_final: 0.7477 (m-70) REVERT: A 250 MET cc_start: 0.8673 (tpp) cc_final: 0.8405 (tpp) REVERT: A 311 LYS cc_start: 0.7657 (tttp) cc_final: 0.6715 (ttpt) REVERT: A 316 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7029 (ptpt) REVERT: A 341 LYS cc_start: 0.8307 (mttm) cc_final: 0.7978 (mtmm) REVERT: B 13 LYS cc_start: 0.8581 (tttm) cc_final: 0.8062 (ttpt) REVERT: B 41 LYS cc_start: 0.7976 (mmtm) cc_final: 0.7415 (mttt) REVERT: B 49 GLU cc_start: 0.7733 (pm20) cc_final: 0.6883 (tp30) REVERT: B 52 GLU cc_start: 0.7890 (tt0) cc_final: 0.7595 (tt0) REVERT: B 303 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7039 (mmp-170) REVERT: B 311 LYS cc_start: 0.7509 (mmtp) cc_final: 0.7068 (ttpt) REVERT: C 42 ARG cc_start: 0.7378 (mtp180) cc_final: 0.6341 (mmp80) REVERT: C 152 LYS cc_start: 0.8014 (tptp) cc_final: 0.7188 (ptpt) REVERT: C 199 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7719 (mmpt) REVERT: C 242 LYS cc_start: 0.7885 (mttt) cc_final: 0.7490 (mptt) REVERT: C 303 ARG cc_start: 0.6943 (mtp-110) cc_final: 0.6327 (ttt-90) REVERT: D 13 LYS cc_start: 0.8427 (tttp) cc_final: 0.8167 (tmmt) REVERT: D 165 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: D 199 LYS cc_start: 0.8413 (mttp) cc_final: 0.7602 (mmpt) REVERT: D 242 LYS cc_start: 0.7853 (mmtm) cc_final: 0.7335 (tppt) REVERT: D 303 ARG cc_start: 0.6906 (ttp80) cc_final: 0.6332 (ttt-90) REVERT: D 341 LYS cc_start: 0.7926 (mttm) cc_final: 0.7168 (mmpt) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.9620 time to fit residues: 109.5960 Evaluate side-chains 106 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 68 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 95 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 = 0.3610 r_free = 0.3610 target = 0.140480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.108393 restraints weight = 10932.713| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.27 r_work: 0.3105 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1760 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= 0.129 Angle : 0.501 6.666 14464 Z= 0.261 Chirality : 0.041 0.145 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.154 55.712 1480 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.26 % Allowed : 8.72 % Favored : 90.02 % 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: 1.73 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 716 sheet: -1.75 (0.34), residues: 204 loop : 0.35 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.024 0.002 TYR D 213 PHE 0.016 0.002 PHE B 144 TRP 0.013 0.002 TRP D 147 HIS 0.004 0.001 HIS D 4 Details of bonding type rmsd covalent geometry : bond 0.00295 (10672) covalent geometry : angle 0.50082 (14464) hydrogen bonds : bond 0.05151 ( 576) hydrogen bonds : angle 4.01961 ( 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 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.474 Fit side-chains REVERT: A 42 ARG cc_start: 0.6835 (mtp180) cc_final: 0.6542 (mmp80) REVERT: A 52 GLU cc_start: 0.7502 (tt0) cc_final: 0.7032 (tt0) REVERT: A 86 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7797 (mtpt) REVERT: A 152 LYS cc_start: 0.8402 (ttmt) cc_final: 0.7824 (tttm) REVERT: A 199 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7621 (mmmt) REVERT: A 237 HIS cc_start: 0.7973 (t-170) cc_final: 0.7459 (m-70) REVERT: A 250 MET cc_start: 0.8677 (tpp) cc_final: 0.8407 (tpp) REVERT: A 311 LYS cc_start: 0.7612 (tttp) cc_final: 0.6658 (ttpt) REVERT: A 316 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7007 (ptpt) REVERT: A 341 LYS cc_start: 0.8275 (mttm) cc_final: 0.7937 (mtmm) REVERT: B 13 LYS cc_start: 0.8554 (tttm) cc_final: 0.8016 (ttpt) REVERT: B 41 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7341 (mttt) REVERT: B 49 GLU cc_start: 0.7724 (pm20) cc_final: 0.6838 (tp30) REVERT: B 52 GLU cc_start: 0.7865 (tt0) cc_final: 0.7574 (tt0) REVERT: B 303 ARG cc_start: 0.7685 (mtp85) cc_final: 0.6998 (mmp-170) REVERT: B 311 LYS cc_start: 0.7485 (mmtp) cc_final: 0.7015 (ttpt) REVERT: C 42 ARG cc_start: 0.7350 (mtp180) cc_final: 0.6292 (mmp80) REVERT: C 152 LYS cc_start: 0.7968 (tptp) cc_final: 0.7107 (ptpt) REVERT: C 199 LYS cc_start: 0.8371 (mtmt) cc_final: 0.7691 (mmpt) REVERT: C 242 LYS cc_start: 0.7870 (mttt) cc_final: 0.7452 (mptt) REVERT: C 303 ARG cc_start: 0.6927 (mtp-110) cc_final: 0.6288 (ttt-90) REVERT: D 13 LYS cc_start: 0.8406 (tttp) cc_final: 0.8135 (tmmt) REVERT: D 165 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: D 199 LYS cc_start: 0.8389 (mttp) cc_final: 0.7558 (mmpt) REVERT: D 242 LYS cc_start: 0.7836 (mmtm) cc_final: 0.7314 (tppt) REVERT: D 303 ARG cc_start: 0.6865 (ttp80) cc_final: 0.6286 (ttt-90) REVERT: D 341 LYS cc_start: 0.7919 (mttm) cc_final: 0.7141 (mmpt) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 1.0032 time to fit residues: 110.9945 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 : 0.447 ------------------------------------------------------------------------------- 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 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 280 SER 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 105 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 110 optimal weight: 0.0980 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 106 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 95 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 = 0.3637 r_free = 0.3637 target = 0.142761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110239 restraints weight = 11000.934| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.28 r_work: 0.3135 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10672 Z= 0.107 Angle : 0.467 6.463 14464 Z= 0.242 Chirality : 0.040 0.135 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.997 55.953 1480 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.35 % Allowed : 8.72 % Favored : 89.93 % 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: 2.69 (0.19), residues: 716 sheet: -1.71 (0.34), residues: 204 loop : 0.42 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 303 TYR 0.020 0.001 TYR D 213 PHE 0.016 0.001 PHE B 144 TRP 0.010 0.001 TRP D 147 HIS 0.003 0.001 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00240 (10672) covalent geometry : angle 0.46670 (14464) hydrogen bonds : bond 0.04500 ( 576) hydrogen bonds : angle 3.91474 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4609.79 seconds wall clock time: 79 minutes 29.20 seconds (4769.20 seconds total)