Starting phenix.real_space_refine on Sun May 3 09:01:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ni_75861/05_2026/11ni_75861.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ni_75861/05_2026/11ni_75861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11ni_75861/05_2026/11ni_75861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ni_75861/05_2026/11ni_75861.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11ni_75861/05_2026/11ni_75861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ni_75861/05_2026/11ni_75861.map" } resolution = 2.27 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 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 11843 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: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 349 Classifications: {'water': 349} Link IDs: {None: 348} Chain: "B" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 345 Classifications: {'water': 345} Link IDs: {None: 344} Chain: "C" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 346 Classifications: {'water': 346} Link IDs: {None: 345} Chain: "D" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 331 Classifications: {'water': 331} Link IDs: {None: 330} Time building chain proxies: 2.70, per 1000 atoms: 0.23 Number of scatterers: 11843 At special positions: 0 Unit cell: (99.225, 80.115, 108.045, 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 3351 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 514.2 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 54.0% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 45 removed outlier: 3.651A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.857A 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: 3.884A 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 removed outlier: 3.528A pdb=" N ASN A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 306 through 314 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: 3.692A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.861A 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 68 through 72 removed outlier: 4.304A pdb=" N CYS B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.862A 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 removed outlier: 3.538A pdb=" N ASN B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 306 through 314 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: 3.671A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.905A pdb=" N TYR C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 removed outlier: 3.520A 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 260 Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 306 through 314 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: 3.703A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.881A 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 68 through 72 removed outlier: 4.317A pdb=" N CYS D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 68 through 72' Processing helix chain 'D' and resid 79 through 84 removed outlier: 3.854A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 removed outlier: 3.529A pdb=" N ASN D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 226 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.722A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA A 32 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.282A 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 31 removed outlier: 6.753A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 32 removed outlier: 6.757A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ALA C 32 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA C 145 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N GLU C 187 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP C 147 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLU C 189 " --> pdb=" O TRP C 147 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N CYS C 149 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU C 191 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU C 151 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 6.227A 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: 6.748A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.292A 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 114 571 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.30 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: 2215 1.33 - 1.45: 2228 1.45 - 1.57: 6168 1.57 - 1.69: 5 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C VAL C 260 " pdb=" N PRO C 261 " ideal model delta sigma weight residual 1.329 1.379 -0.050 1.18e-02 7.18e+03 1.79e+01 bond pdb=" N VAL B 264 " pdb=" CA VAL B 264 " ideal model delta sigma weight residual 1.457 1.500 -0.044 1.19e-02 7.06e+03 1.34e+01 bond pdb=" N VAL A 264 " pdb=" CA VAL A 264 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.19e-02 7.06e+03 1.32e+01 bond pdb=" N PHE A 144 " pdb=" CA PHE A 144 " ideal model delta sigma weight residual 1.454 1.497 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C VAL D 260 " pdb=" N PRO D 261 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.18e-02 7.18e+03 1.04e+01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 13293 1.30 - 2.60: 963 2.60 - 3.89: 157 3.89 - 5.19: 40 5.19 - 6.49: 11 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PHE C 144 " pdb=" CB PHE C 144 " pdb=" CG PHE C 144 " ideal model delta sigma weight residual 113.80 118.45 -4.65 1.00e+00 1.00e+00 2.16e+01 angle pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " pdb=" CG PHE B 144 " ideal model delta sigma weight residual 113.80 118.41 -4.61 1.00e+00 1.00e+00 2.13e+01 angle pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " pdb=" CG PHE D 144 " ideal model delta sigma weight residual 113.80 118.35 -4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA PRO B 188 " pdb=" N PRO B 188 " pdb=" CD PRO B 188 " ideal model delta sigma weight residual 112.00 106.06 5.94 1.40e+00 5.10e-01 1.80e+01 angle pdb=" N PRO C 261 " pdb=" CA PRO C 261 " pdb=" C PRO C 261 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.80e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6045 17.98 - 35.96: 337 35.96 - 53.94: 94 53.94 - 71.92: 18 71.92 - 89.91: 10 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CA PHE C 299 " pdb=" C PHE C 299 " pdb=" N SER C 300 " pdb=" CA SER C 300 " ideal model delta harmonic sigma weight residual 180.00 162.59 17.41 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA PHE B 299 " pdb=" C PHE B 299 " pdb=" N SER B 300 " pdb=" CA SER B 300 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PHE A 299 " pdb=" C PHE A 299 " pdb=" N SER A 300 " pdb=" CA SER A 300 " ideal model delta harmonic sigma weight residual 180.00 163.39 16.61 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1348 0.060 - 0.120: 238 0.120 - 0.180: 43 0.180 - 0.239: 13 0.239 - 0.299: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA LEU C 61 " pdb=" N LEU C 61 " pdb=" C LEU C 61 " pdb=" CB LEU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LEU B 61 " pdb=" N LEU B 61 " pdb=" C LEU B 61 " pdb=" CB LEU B 61 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " 0.071 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO B 261 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 260 " -0.022 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C VAL C 260 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL C 260 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO C 261 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 260 " 0.021 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C VAL A 260 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL A 260 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO A 261 " 0.024 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2082 2.76 - 3.29: 12122 3.29 - 3.83: 23124 3.83 - 4.36: 28440 4.36 - 4.90: 43598 Nonbonded interactions: 109366 Sorted by model distance: nonbonded pdb=" O GLN C 60 " pdb=" OG1 THR C 64 " model vdw 2.222 3.040 nonbonded pdb=" O GLN A 60 " pdb=" OG1 THR A 64 " model vdw 2.265 3.040 nonbonded pdb=" O GLN D 60 " pdb=" OG1 THR D 64 " model vdw 2.267 3.040 nonbonded pdb=" O GLN B 60 " pdb=" OG1 THR B 64 " model vdw 2.268 3.040 nonbonded pdb=" O ARG A 42 " pdb=" OG SER A 45 " model vdw 2.284 3.040 ... (remaining 109361 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: 4.750 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 0.088 10672 Z= 0.316 Angle : 0.758 6.488 14464 Z= 0.474 Chirality : 0.051 0.299 1644 Planarity : 0.006 0.110 1880 Dihedral : 12.911 89.906 3984 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.17 % Allowed : 1.26 % Favored : 97.57 % 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: 1.21 (0.23), residues: 1364 helix: 1.84 (0.19), residues: 700 sheet: -1.09 (0.33), residues: 224 loop : 0.34 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 330 TYR 0.021 0.002 TYR B 213 PHE 0.024 0.003 PHE C 144 TRP 0.042 0.005 TRP B 147 HIS 0.013 0.003 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00533 (10672) covalent geometry : angle 0.75754 (14464) hydrogen bonds : bond 0.14414 ( 571) hydrogen bonds : angle 5.62511 ( 1665) *********************** 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 206 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.400 Fit side-chains REVERT: A 53 GLU cc_start: 0.7489 (tp30) cc_final: 0.7273 (tp30) REVERT: A 242 LYS cc_start: 0.7748 (mmtt) cc_final: 0.7074 (tmtt) REVERT: A 295 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.6052 (m-90) REVERT: A 303 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6317 (mtm-85) REVERT: A 311 LYS cc_start: 0.6882 (mmtp) cc_final: 0.6304 (ttpp) REVERT: B 52 GLU cc_start: 0.6845 (tt0) cc_final: 0.6120 (tm-30) REVERT: B 237 HIS cc_start: 0.7464 (t70) cc_final: 0.7113 (m90) REVERT: B 242 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7167 (tmtt) REVERT: B 295 TRP cc_start: 0.8133 (OUTLIER) cc_final: 0.6071 (m-90) REVERT: B 303 ARG cc_start: 0.7518 (mtp180) cc_final: 0.6444 (mmp80) REVERT: B 311 LYS cc_start: 0.6861 (mmtp) cc_final: 0.6369 (ttpp) REVERT: C 242 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7139 (tmtt) REVERT: C 295 TRP cc_start: 0.8040 (OUTLIER) cc_final: 0.5898 (m-90) REVERT: C 303 ARG cc_start: 0.7777 (mtt180) cc_final: 0.6379 (mtm-85) REVERT: C 311 LYS cc_start: 0.7035 (tptm) cc_final: 0.6151 (ttpp) REVERT: D 52 GLU cc_start: 0.6933 (tt0) cc_final: 0.6230 (tm-30) REVERT: D 237 HIS cc_start: 0.7442 (t70) cc_final: 0.7075 (m90) REVERT: D 242 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7168 (tmtt) REVERT: D 246 GLU cc_start: 0.8030 (mp0) cc_final: 0.7793 (mp0) REVERT: D 295 TRP cc_start: 0.8098 (OUTLIER) cc_final: 0.6151 (m-90) REVERT: D 303 ARG cc_start: 0.7240 (ttm-80) cc_final: 0.6616 (mtm-85) REVERT: D 311 LYS cc_start: 0.6889 (mmtp) cc_final: 0.6438 (ttpp) outliers start: 13 outliers final: 1 residues processed: 205 average time/residue: 0.8898 time to fit residues: 192.5497 Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU 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: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0060 chunk 55 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 168 ASN A 274 GLN B 274 GLN C 136 GLN C 168 ASN C 306 GLN D 168 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.163990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129194 restraints weight = 9615.938| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.15 r_work: 0.3281 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10672 Z= 0.111 Angle : 0.488 8.036 14464 Z= 0.260 Chirality : 0.040 0.154 1644 Planarity : 0.004 0.056 1880 Dihedral : 4.710 41.580 1482 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.62 % Allowed : 7.64 % 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: 2.01 (0.24), residues: 1364 helix: 2.67 (0.19), residues: 712 sheet: -1.17 (0.32), residues: 232 loop : 0.63 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 330 TYR 0.017 0.002 TYR B 213 PHE 0.010 0.001 PHE D 144 TRP 0.012 0.001 TRP A 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00237 (10672) covalent geometry : angle 0.48847 (14464) hydrogen bonds : bond 0.04385 ( 571) hydrogen bonds : angle 4.22260 ( 1665) *********************** 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 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.468 Fit side-chains REVERT: A 53 GLU cc_start: 0.7609 (tp30) cc_final: 0.7369 (tp30) REVERT: A 242 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7277 (tmtt) REVERT: A 295 TRP cc_start: 0.8484 (OUTLIER) cc_final: 0.6218 (m-90) REVERT: A 303 ARG cc_start: 0.8081 (mtt180) cc_final: 0.6767 (ttp-110) REVERT: A 311 LYS cc_start: 0.7061 (mmtp) cc_final: 0.6547 (ttpp) REVERT: B 52 GLU cc_start: 0.6824 (tt0) cc_final: 0.6183 (tm-30) REVERT: B 237 HIS cc_start: 0.7349 (t70) cc_final: 0.7052 (m90) REVERT: B 242 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7241 (tmtt) REVERT: B 295 TRP cc_start: 0.8488 (OUTLIER) cc_final: 0.6225 (m-90) REVERT: B 303 ARG cc_start: 0.7620 (mtp180) cc_final: 0.6734 (mmp80) REVERT: B 311 LYS cc_start: 0.7050 (mmtp) cc_final: 0.6582 (ttpp) REVERT: C 237 HIS cc_start: 0.7428 (t-90) cc_final: 0.7044 (m90) REVERT: C 242 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7281 (mttt) REVERT: C 295 TRP cc_start: 0.8458 (OUTLIER) cc_final: 0.6114 (m-90) REVERT: C 303 ARG cc_start: 0.7937 (mtt180) cc_final: 0.6693 (ttp-110) REVERT: C 311 LYS cc_start: 0.7139 (tptm) cc_final: 0.6340 (ttpp) REVERT: C 325 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6565 (tp30) REVERT: D 52 GLU cc_start: 0.6812 (tt0) cc_final: 0.6243 (tm-30) REVERT: D 237 HIS cc_start: 0.7314 (t70) cc_final: 0.7045 (m90) REVERT: D 242 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7179 (tmtt) REVERT: D 246 GLU cc_start: 0.7987 (mp0) cc_final: 0.7779 (mp0) REVERT: D 292 LEU cc_start: 0.8258 (tp) cc_final: 0.8013 (tt) REVERT: D 295 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.5874 (m-90) REVERT: D 303 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.6594 (ttp-110) REVERT: D 311 LYS cc_start: 0.7019 (mmtp) cc_final: 0.6545 (ttpp) REVERT: D 329 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7609 (mtmm) outliers start: 18 outliers final: 3 residues processed: 142 average time/residue: 0.8542 time to fit residues: 128.6875 Evaluate side-chains 123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 295 TRP Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123143 restraints weight = 9578.053| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.06 r_work: 0.3224 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10672 Z= 0.114 Angle : 0.496 8.817 14464 Z= 0.263 Chirality : 0.040 0.152 1644 Planarity : 0.004 0.035 1880 Dihedral : 4.893 46.488 1480 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.71 % Allowed : 8.72 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.23), residues: 1364 helix: 2.81 (0.19), residues: 712 sheet: -1.14 (0.32), residues: 232 loop : 0.66 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 257 TYR 0.022 0.002 TYR C 213 PHE 0.011 0.002 PHE D 144 TRP 0.018 0.002 TRP A 147 HIS 0.004 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00244 (10672) covalent geometry : angle 0.49563 (14464) hydrogen bonds : bond 0.04954 ( 571) hydrogen bonds : angle 4.21566 ( 1665) *********************** 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 135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.486 Fit side-chains REVERT: A 53 GLU cc_start: 0.7708 (tp30) cc_final: 0.7431 (tp30) REVERT: A 60 GLN cc_start: 0.8473 (tt0) cc_final: 0.8259 (tt0) REVERT: A 242 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7266 (tmtt) REVERT: A 292 LEU cc_start: 0.8477 (tp) cc_final: 0.8219 (tt) REVERT: A 295 TRP cc_start: 0.8714 (OUTLIER) cc_final: 0.6381 (m-90) REVERT: A 303 ARG cc_start: 0.8030 (mtt180) cc_final: 0.6768 (ttp-110) REVERT: A 311 LYS cc_start: 0.7038 (mmtp) cc_final: 0.6555 (ttpp) REVERT: A 330 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.6757 (mmm160) REVERT: A 341 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8297 (mtmt) REVERT: B 52 GLU cc_start: 0.6865 (tt0) cc_final: 0.6250 (tm-30) REVERT: B 237 HIS cc_start: 0.7382 (t70) cc_final: 0.7075 (m90) REVERT: B 242 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7250 (tmtt) REVERT: B 295 TRP cc_start: 0.8716 (OUTLIER) cc_final: 0.6396 (m-90) REVERT: B 303 ARG cc_start: 0.7655 (mtp180) cc_final: 0.6829 (mmp80) REVERT: B 311 LYS cc_start: 0.7044 (mmtp) cc_final: 0.6584 (ttpp) REVERT: C 292 LEU cc_start: 0.8370 (tp) cc_final: 0.8091 (tt) REVERT: C 295 TRP cc_start: 0.8722 (OUTLIER) cc_final: 0.6459 (m-90) REVERT: C 303 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6731 (ttp-110) REVERT: C 311 LYS cc_start: 0.7291 (tptm) cc_final: 0.6371 (ttpp) REVERT: C 320 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6895 (tp) REVERT: C 325 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: C 326 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7836 (mm-30) REVERT: C 341 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8329 (mtmt) REVERT: D 52 GLU cc_start: 0.6883 (tt0) cc_final: 0.6360 (tm-30) REVERT: D 237 HIS cc_start: 0.7368 (t70) cc_final: 0.7089 (m90) REVERT: D 242 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7174 (tmtt) REVERT: D 246 GLU cc_start: 0.7978 (mp0) cc_final: 0.7724 (mp0) REVERT: D 292 LEU cc_start: 0.8403 (tp) cc_final: 0.8137 (tt) REVERT: D 295 TRP cc_start: 0.8686 (OUTLIER) cc_final: 0.6352 (m-90) REVERT: D 303 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.6713 (ttp-110) REVERT: D 311 LYS cc_start: 0.7029 (mmtp) cc_final: 0.6526 (ttpp) REVERT: D 329 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7688 (mtmm) REVERT: D 341 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8296 (mtmt) outliers start: 19 outliers final: 5 residues processed: 131 average time/residue: 0.8688 time to fit residues: 120.6766 Evaluate side-chains 117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.158644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121676 restraints weight = 9621.240| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.08 r_work: 0.3201 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1838 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= 0.118 Angle : 0.503 8.638 14464 Z= 0.267 Chirality : 0.041 0.155 1644 Planarity : 0.004 0.034 1880 Dihedral : 5.052 49.002 1480 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.71 % Allowed : 8.54 % Favored : 89.75 % 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: 2.17 (0.23), residues: 1364 helix: 2.84 (0.19), residues: 712 sheet: -1.18 (0.32), residues: 232 loop : 0.68 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 330 TYR 0.023 0.002 TYR C 213 PHE 0.013 0.002 PHE D 144 TRP 0.016 0.002 TRP A 147 HIS 0.005 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00256 (10672) covalent geometry : angle 0.50312 (14464) hydrogen bonds : bond 0.05044 ( 571) hydrogen bonds : angle 4.26115 ( 1665) *********************** 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 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.465 Fit side-chains REVERT: A 53 GLU cc_start: 0.7689 (tp30) cc_final: 0.7394 (tp30) REVERT: A 60 GLN cc_start: 0.8465 (tt0) cc_final: 0.8259 (tt0) REVERT: A 242 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7253 (tmtt) REVERT: A 292 LEU cc_start: 0.8496 (tp) cc_final: 0.8212 (tt) REVERT: A 295 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.6573 (m-90) REVERT: A 303 ARG cc_start: 0.8082 (mtt180) cc_final: 0.6791 (ttp-110) REVERT: A 311 LYS cc_start: 0.7076 (mmtp) cc_final: 0.6529 (ttpp) REVERT: A 326 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 341 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8295 (mtmt) REVERT: B 52 GLU cc_start: 0.6896 (tt0) cc_final: 0.6245 (tm-30) REVERT: B 237 HIS cc_start: 0.7397 (t70) cc_final: 0.7060 (m90) REVERT: B 242 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7262 (tmtt) REVERT: B 295 TRP cc_start: 0.8780 (OUTLIER) cc_final: 0.6584 (m-90) REVERT: B 303 ARG cc_start: 0.7761 (mtp180) cc_final: 0.6867 (mmp80) REVERT: B 311 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6607 (ttpp) REVERT: B 316 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7666 (mttp) REVERT: B 341 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8281 (mtmt) REVERT: C 292 LEU cc_start: 0.8452 (tp) cc_final: 0.8169 (tt) REVERT: C 295 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.6491 (m-90) REVERT: C 303 ARG cc_start: 0.7936 (mtt180) cc_final: 0.6769 (ttp-110) REVERT: C 311 LYS cc_start: 0.7318 (tptm) cc_final: 0.6374 (ttpp) REVERT: C 320 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6961 (tp) REVERT: C 326 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 341 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8287 (mtmt) REVERT: D 52 GLU cc_start: 0.6864 (tt0) cc_final: 0.6347 (tm-30) REVERT: D 237 HIS cc_start: 0.7405 (t70) cc_final: 0.7085 (m90) REVERT: D 242 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7233 (tmtt) REVERT: D 246 GLU cc_start: 0.8017 (mp0) cc_final: 0.7760 (mp0) REVERT: D 292 LEU cc_start: 0.8447 (tp) cc_final: 0.8188 (tt) REVERT: D 295 TRP cc_start: 0.8802 (OUTLIER) cc_final: 0.6478 (m-90) REVERT: D 303 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.6761 (ttp-110) REVERT: D 311 LYS cc_start: 0.7071 (mmtp) cc_final: 0.6486 (ttpp) REVERT: D 326 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7727 (mm-30) REVERT: D 329 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7716 (mtmt) REVERT: D 341 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8300 (mtmt) outliers start: 19 outliers final: 6 residues processed: 130 average time/residue: 0.8715 time to fit residues: 120.0685 Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 271 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 102 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 8 optimal weight: 0.0770 chunk 111 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN D 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.161088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124573 restraints weight = 9553.315| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.06 r_work: 0.3240 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10672 Z= 0.100 Angle : 0.466 9.150 14464 Z= 0.243 Chirality : 0.039 0.144 1644 Planarity : 0.003 0.034 1880 Dihedral : 4.830 48.450 1480 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.62 % Allowed : 8.81 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.23), residues: 1364 helix: 2.94 (0.19), residues: 712 sheet: -1.21 (0.31), residues: 232 loop : 0.69 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.016 0.001 TYR C 213 PHE 0.013 0.001 PHE D 144 TRP 0.011 0.001 TRP A 147 HIS 0.003 0.001 HIS A 4 Details of bonding type rmsd covalent geometry : bond 0.00216 (10672) covalent geometry : angle 0.46602 (14464) hydrogen bonds : bond 0.04372 ( 571) hydrogen bonds : angle 4.10685 ( 1665) *********************** 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 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.439 Fit side-chains REVERT: A 53 GLU cc_start: 0.7671 (tp30) cc_final: 0.7380 (tp30) REVERT: A 60 GLN cc_start: 0.8485 (tt0) cc_final: 0.8273 (tt0) REVERT: A 242 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7258 (tmtt) REVERT: A 292 LEU cc_start: 0.8497 (tp) cc_final: 0.8219 (tt) REVERT: A 295 TRP cc_start: 0.8732 (OUTLIER) cc_final: 0.6527 (m-90) REVERT: A 303 ARG cc_start: 0.8035 (mtt180) cc_final: 0.6765 (ttp-110) REVERT: A 311 LYS cc_start: 0.7073 (mmtp) cc_final: 0.6523 (ttpp) REVERT: A 341 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8291 (mtmt) REVERT: B 52 GLU cc_start: 0.6921 (tt0) cc_final: 0.6280 (tm-30) REVERT: B 237 HIS cc_start: 0.7366 (t70) cc_final: 0.7060 (m90) REVERT: B 242 LYS cc_start: 0.7893 (mmtt) cc_final: 0.7273 (tmtt) REVERT: B 295 TRP cc_start: 0.8743 (OUTLIER) cc_final: 0.6540 (m-90) REVERT: B 303 ARG cc_start: 0.7729 (mtp180) cc_final: 0.6839 (mmp80) REVERT: B 311 LYS cc_start: 0.7106 (mmtp) cc_final: 0.6566 (ttpp) REVERT: C 292 LEU cc_start: 0.8466 (tp) cc_final: 0.8183 (tt) REVERT: C 295 TRP cc_start: 0.8759 (OUTLIER) cc_final: 0.6530 (m-90) REVERT: C 303 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6728 (ttp-110) REVERT: C 311 LYS cc_start: 0.7359 (tptm) cc_final: 0.6477 (ttpp) REVERT: C 326 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 341 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8298 (mtmt) REVERT: D 52 GLU cc_start: 0.6871 (tt0) cc_final: 0.6347 (tm-30) REVERT: D 237 HIS cc_start: 0.7371 (t70) cc_final: 0.7089 (m90) REVERT: D 242 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7204 (tmtt) REVERT: D 246 GLU cc_start: 0.8042 (mp0) cc_final: 0.7803 (mp0) REVERT: D 292 LEU cc_start: 0.8457 (tp) cc_final: 0.8195 (tt) REVERT: D 295 TRP cc_start: 0.8764 (OUTLIER) cc_final: 0.6600 (m-90) REVERT: D 303 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.6776 (ttp-110) REVERT: D 311 LYS cc_start: 0.7059 (mmtp) cc_final: 0.6491 (ttpp) REVERT: D 341 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8315 (mtmt) outliers start: 18 outliers final: 7 residues processed: 130 average time/residue: 0.8348 time to fit residues: 115.2016 Evaluate side-chains 118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 66 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116319 restraints weight = 9501.036| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.06 r_work: 0.3128 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10672 Z= 0.203 Angle : 0.629 8.272 14464 Z= 0.337 Chirality : 0.048 0.174 1644 Planarity : 0.005 0.038 1880 Dihedral : 5.626 51.457 1480 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.16 % Allowed : 8.18 % Favored : 89.66 % 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: 1.91 (0.23), residues: 1364 helix: 2.57 (0.19), residues: 712 sheet: -1.21 (0.32), residues: 232 loop : 0.61 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 257 TYR 0.032 0.003 TYR C 213 PHE 0.017 0.003 PHE D 144 TRP 0.021 0.003 TRP A 147 HIS 0.009 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00462 (10672) covalent geometry : angle 0.62863 (14464) hydrogen bonds : bond 0.06873 ( 571) hydrogen bonds : angle 4.60816 ( 1665) *********************** 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 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7840 (tp30) cc_final: 0.7463 (tp30) REVERT: A 242 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7309 (tmtt) REVERT: A 292 LEU cc_start: 0.8499 (tp) cc_final: 0.8243 (tt) REVERT: A 303 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7002 (ttp-110) REVERT: A 326 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 330 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.6801 (mmm160) REVERT: A 341 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8284 (mtmt) REVERT: B 52 GLU cc_start: 0.6908 (tt0) cc_final: 0.6246 (tm-30) REVERT: B 237 HIS cc_start: 0.7441 (t70) cc_final: 0.7070 (m90) REVERT: B 242 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7293 (tmtt) REVERT: B 292 LEU cc_start: 0.8469 (tp) cc_final: 0.8239 (tt) REVERT: B 303 ARG cc_start: 0.8002 (mtp180) cc_final: 0.7048 (mmp80) REVERT: B 325 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6678 (tp30) REVERT: C 292 LEU cc_start: 0.8534 (tp) cc_final: 0.8255 (tt) REVERT: C 303 ARG cc_start: 0.8100 (mtt180) cc_final: 0.6945 (ttp-110) REVERT: C 311 LYS cc_start: 0.7597 (tptm) cc_final: 0.6439 (ttpp) REVERT: C 341 LYS cc_start: 0.8502 (mtmm) cc_final: 0.8271 (mtmt) REVERT: D 52 GLU cc_start: 0.6875 (tt0) cc_final: 0.6339 (tm-30) REVERT: D 152 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8380 (pttt) REVERT: D 237 HIS cc_start: 0.7471 (t70) cc_final: 0.7112 (m90) REVERT: D 242 LYS cc_start: 0.7959 (mmtt) cc_final: 0.7255 (tmtt) REVERT: D 246 GLU cc_start: 0.8018 (mp0) cc_final: 0.7785 (mp0) REVERT: D 292 LEU cc_start: 0.8492 (tp) cc_final: 0.8239 (tt) REVERT: D 311 LYS cc_start: 0.7240 (mmtp) cc_final: 0.6588 (ttpp) REVERT: D 325 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6641 (tp30) REVERT: D 341 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8299 (mtmt) outliers start: 24 outliers final: 11 residues processed: 124 average time/residue: 0.9242 time to fit residues: 121.1597 Evaluate side-chains 110 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 316 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.158163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121301 restraints weight = 9543.341| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.06 r_work: 0.3190 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10672 Z= 0.112 Angle : 0.491 7.863 14464 Z= 0.261 Chirality : 0.040 0.149 1644 Planarity : 0.004 0.036 1880 Dihedral : 5.186 51.287 1480 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.35 % Allowed : 9.26 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.23), residues: 1364 helix: 2.79 (0.19), residues: 712 sheet: -1.22 (0.31), residues: 232 loop : 0.63 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 330 TYR 0.020 0.002 TYR A 213 PHE 0.014 0.002 PHE D 144 TRP 0.014 0.001 TRP A 147 HIS 0.004 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00240 (10672) covalent geometry : angle 0.49125 (14464) hydrogen bonds : bond 0.04884 ( 571) hydrogen bonds : angle 4.31307 ( 1665) *********************** 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 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7705 (tp30) cc_final: 0.7383 (tp30) REVERT: A 242 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7268 (tmtt) REVERT: A 292 LEU cc_start: 0.8484 (tp) cc_final: 0.8224 (tt) REVERT: A 303 ARG cc_start: 0.8119 (mtt180) cc_final: 0.6844 (ttp-110) REVERT: A 311 LYS cc_start: 0.7162 (mmtp) cc_final: 0.6552 (ttpp) REVERT: A 326 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 341 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8279 (mtmt) REVERT: B 52 GLU cc_start: 0.6872 (tt0) cc_final: 0.6244 (tm-30) REVERT: B 237 HIS cc_start: 0.7430 (t70) cc_final: 0.7078 (m90) REVERT: B 242 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7266 (tmtt) REVERT: B 292 LEU cc_start: 0.8436 (tp) cc_final: 0.8212 (tt) REVERT: B 303 ARG cc_start: 0.7813 (mtp180) cc_final: 0.6903 (mmp80) REVERT: B 311 LYS cc_start: 0.7215 (mmtp) cc_final: 0.6624 (ttpp) REVERT: B 325 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6666 (tp30) REVERT: C 292 LEU cc_start: 0.8501 (tp) cc_final: 0.8225 (tt) REVERT: C 303 ARG cc_start: 0.7950 (mtt180) cc_final: 0.6786 (ttp-110) REVERT: C 311 LYS cc_start: 0.7596 (tptm) cc_final: 0.6524 (ttpp) REVERT: C 341 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8259 (mtmt) REVERT: D 52 GLU cc_start: 0.6823 (tt0) cc_final: 0.6275 (tm-30) REVERT: D 237 HIS cc_start: 0.7415 (t70) cc_final: 0.7076 (m90) REVERT: D 242 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7233 (tmtt) REVERT: D 246 GLU cc_start: 0.8018 (mp0) cc_final: 0.7745 (mp0) REVERT: D 292 LEU cc_start: 0.8469 (tp) cc_final: 0.8223 (tt) REVERT: D 311 LYS cc_start: 0.7198 (mmtp) cc_final: 0.6593 (ttpp) REVERT: D 316 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7777 (mttp) REVERT: D 325 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6638 (tp30) REVERT: D 330 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.6865 (mmm160) REVERT: D 341 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8278 (mtmt) outliers start: 15 outliers final: 10 residues processed: 125 average time/residue: 0.8543 time to fit residues: 113.2913 Evaluate side-chains 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 116 optimal weight: 0.4980 chunk 110 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.119989 restraints weight = 9525.365| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.06 r_work: 0.3175 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10672 Z= 0.127 Angle : 0.519 8.720 14464 Z= 0.274 Chirality : 0.041 0.158 1644 Planarity : 0.004 0.039 1880 Dihedral : 5.273 51.935 1480 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.44 % Allowed : 9.35 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.23), residues: 1364 helix: 2.78 (0.19), residues: 712 sheet: -1.20 (0.32), residues: 232 loop : 0.63 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.022 0.002 TYR C 213 PHE 0.015 0.002 PHE D 144 TRP 0.015 0.002 TRP A 147 HIS 0.004 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00277 (10672) covalent geometry : angle 0.51869 (14464) hydrogen bonds : bond 0.05291 ( 571) hydrogen bonds : angle 4.32146 ( 1665) *********************** 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 127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.484 Fit side-chains REVERT: A 53 GLU cc_start: 0.7707 (tp30) cc_final: 0.7387 (tp30) REVERT: A 242 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7599 (mttm) REVERT: A 292 LEU cc_start: 0.8465 (tp) cc_final: 0.8221 (tt) REVERT: A 303 ARG cc_start: 0.8158 (mtt180) cc_final: 0.6877 (ttp-110) REVERT: A 311 LYS cc_start: 0.7184 (mmtp) cc_final: 0.6552 (ttpp) REVERT: A 326 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 330 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.6772 (mmm160) REVERT: A 341 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8278 (mtmt) REVERT: B 52 GLU cc_start: 0.6903 (tt0) cc_final: 0.6261 (tm-30) REVERT: B 237 HIS cc_start: 0.7432 (t70) cc_final: 0.7073 (m90) REVERT: B 242 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7296 (tmtt) REVERT: B 292 LEU cc_start: 0.8430 (tp) cc_final: 0.8202 (tt) REVERT: B 303 ARG cc_start: 0.7907 (mtp180) cc_final: 0.6915 (mmp80) REVERT: B 311 LYS cc_start: 0.7240 (mmtp) cc_final: 0.6626 (ttpp) REVERT: B 316 LYS cc_start: 0.8081 (mttm) cc_final: 0.7685 (mmtp) REVERT: B 325 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6666 (tp30) REVERT: C 292 LEU cc_start: 0.8511 (tp) cc_final: 0.8228 (tt) REVERT: C 303 ARG cc_start: 0.7991 (mtt180) cc_final: 0.6829 (ttp-110) REVERT: C 311 LYS cc_start: 0.7615 (tptm) cc_final: 0.6465 (ttpp) REVERT: C 341 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8260 (mtmt) REVERT: D 52 GLU cc_start: 0.6831 (tt0) cc_final: 0.6288 (tm-30) REVERT: D 237 HIS cc_start: 0.7429 (t70) cc_final: 0.7079 (m90) REVERT: D 242 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7254 (tmtt) REVERT: D 246 GLU cc_start: 0.8040 (mp0) cc_final: 0.7833 (mp0) REVERT: D 292 LEU cc_start: 0.8473 (tp) cc_final: 0.8228 (tt) REVERT: D 303 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.6865 (ttt-90) REVERT: D 311 LYS cc_start: 0.7228 (mmtp) cc_final: 0.6580 (ttpp) REVERT: D 316 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7737 (mttp) REVERT: D 325 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: D 330 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.6775 (mmm160) REVERT: D 341 LYS cc_start: 0.8520 (mtmm) cc_final: 0.8299 (mtmt) outliers start: 16 outliers final: 10 residues processed: 123 average time/residue: 0.8911 time to fit residues: 116.0327 Evaluate side-chains 117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118766 restraints weight = 9394.811| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.07 r_work: 0.3160 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10672 Z= 0.141 Angle : 0.543 8.779 14464 Z= 0.287 Chirality : 0.043 0.159 1644 Planarity : 0.004 0.037 1880 Dihedral : 5.388 52.116 1480 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.35 % Allowed : 9.35 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.23), residues: 1364 helix: 2.73 (0.19), residues: 712 sheet: -1.19 (0.32), residues: 232 loop : 0.61 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.025 0.002 TYR C 213 PHE 0.015 0.002 PHE D 144 TRP 0.016 0.002 TRP A 147 HIS 0.005 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00311 (10672) covalent geometry : angle 0.54290 (14464) hydrogen bonds : bond 0.05653 ( 571) hydrogen bonds : angle 4.39374 ( 1665) *********************** 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 123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.444 Fit side-chains REVERT: A 53 GLU cc_start: 0.7730 (tp30) cc_final: 0.7399 (tp30) REVERT: A 242 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7591 (mttm) REVERT: A 292 LEU cc_start: 0.8473 (tp) cc_final: 0.8225 (tt) REVERT: A 303 ARG cc_start: 0.8179 (mtt180) cc_final: 0.6901 (ttp-110) REVERT: A 311 LYS cc_start: 0.7201 (mmtp) cc_final: 0.6542 (ttpp) REVERT: A 326 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 330 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.6749 (mmm160) REVERT: A 341 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8283 (mtmt) REVERT: B 52 GLU cc_start: 0.6894 (tt0) cc_final: 0.6252 (tm-30) REVERT: B 237 HIS cc_start: 0.7440 (t70) cc_final: 0.7072 (m90) REVERT: B 242 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7578 (mttm) REVERT: B 292 LEU cc_start: 0.8435 (tp) cc_final: 0.8206 (tt) REVERT: B 303 ARG cc_start: 0.7952 (mtp180) cc_final: 0.6945 (mmp80) REVERT: B 311 LYS cc_start: 0.7291 (mmtp) cc_final: 0.6647 (ttpp) REVERT: B 325 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6723 (tp30) REVERT: C 292 LEU cc_start: 0.8517 (tp) cc_final: 0.8235 (tt) REVERT: C 303 ARG cc_start: 0.8017 (mtt180) cc_final: 0.6860 (ttp-110) REVERT: C 311 LYS cc_start: 0.7635 (tptm) cc_final: 0.6465 (ttpp) REVERT: C 341 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8261 (mtmt) REVERT: D 52 GLU cc_start: 0.6896 (tt0) cc_final: 0.6332 (tm-30) REVERT: D 237 HIS cc_start: 0.7453 (t70) cc_final: 0.7097 (m90) REVERT: D 242 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7571 (mttm) REVERT: D 246 GLU cc_start: 0.8029 (mp0) cc_final: 0.7792 (mp0) REVERT: D 292 LEU cc_start: 0.8472 (tp) cc_final: 0.8226 (tt) REVERT: D 303 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.6887 (ttt-90) REVERT: D 311 LYS cc_start: 0.7259 (mmtp) cc_final: 0.6589 (ttpp) REVERT: D 325 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: D 330 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.6745 (mmm160) REVERT: D 341 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8300 (mtmt) outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 0.9117 time to fit residues: 113.7563 Evaluate side-chains 120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 26 optimal weight: 0.0470 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119394 restraints weight = 9547.232| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.06 r_work: 0.3168 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10672 Z= 0.134 Angle : 0.531 8.721 14464 Z= 0.281 Chirality : 0.042 0.158 1644 Planarity : 0.004 0.037 1880 Dihedral : 5.358 52.270 1480 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.44 % Allowed : 9.35 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.23), residues: 1364 helix: 2.73 (0.19), residues: 712 sheet: -1.21 (0.32), residues: 232 loop : 0.62 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 330 TYR 0.023 0.002 TYR C 213 PHE 0.015 0.002 PHE D 144 TRP 0.015 0.002 TRP A 147 HIS 0.005 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00295 (10672) covalent geometry : angle 0.53105 (14464) hydrogen bonds : bond 0.05455 ( 571) hydrogen bonds : angle 4.37106 ( 1665) ********************** 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 125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.405 Fit side-chains REVERT: A 53 GLU cc_start: 0.7711 (tp30) cc_final: 0.7387 (tp30) REVERT: A 242 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7580 (mttm) REVERT: A 292 LEU cc_start: 0.8471 (tp) cc_final: 0.8224 (tt) REVERT: A 303 ARG cc_start: 0.8161 (mtt180) cc_final: 0.6889 (ttp-110) REVERT: A 311 LYS cc_start: 0.7235 (mmtp) cc_final: 0.6564 (ttpp) REVERT: A 326 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7811 (mm-30) REVERT: A 330 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.6740 (mmm160) REVERT: A 341 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8280 (mtmt) REVERT: B 52 GLU cc_start: 0.6916 (tt0) cc_final: 0.6277 (tm-30) REVERT: B 237 HIS cc_start: 0.7440 (t70) cc_final: 0.7077 (m90) REVERT: B 242 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7565 (mttm) REVERT: B 292 LEU cc_start: 0.8435 (tp) cc_final: 0.8208 (tt) REVERT: B 303 ARG cc_start: 0.7928 (mtp180) cc_final: 0.6911 (mmp80) REVERT: B 311 LYS cc_start: 0.7279 (mmtp) cc_final: 0.6647 (ttpp) REVERT: B 325 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6716 (tp30) REVERT: C 292 LEU cc_start: 0.8521 (tp) cc_final: 0.8239 (tt) REVERT: C 303 ARG cc_start: 0.7990 (mtt180) cc_final: 0.6843 (ttp-110) REVERT: C 311 LYS cc_start: 0.7622 (tptm) cc_final: 0.6465 (ttpp) REVERT: C 341 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8264 (mtmt) REVERT: D 52 GLU cc_start: 0.6892 (tt0) cc_final: 0.6328 (tm-30) REVERT: D 237 HIS cc_start: 0.7447 (t70) cc_final: 0.7086 (m90) REVERT: D 242 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7569 (mttm) REVERT: D 246 GLU cc_start: 0.8030 (mp0) cc_final: 0.7735 (mp0) REVERT: D 292 LEU cc_start: 0.8475 (tp) cc_final: 0.8229 (tt) REVERT: D 303 ARG cc_start: 0.7760 (ttm-80) cc_final: 0.6847 (ttt-90) REVERT: D 311 LYS cc_start: 0.7281 (mmtp) cc_final: 0.6618 (ttpp) REVERT: D 325 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6723 (tp30) REVERT: D 330 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.6753 (mmm160) REVERT: D 341 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8299 (mtmt) outliers start: 16 outliers final: 12 residues processed: 120 average time/residue: 0.9021 time to fit residues: 114.7001 Evaluate side-chains 120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 316 LYS Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 330 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN D 241 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118644 restraints weight = 9480.946| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.07 r_work: 0.3158 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10672 Z= 0.141 Angle : 0.544 8.614 14464 Z= 0.288 Chirality : 0.043 0.159 1644 Planarity : 0.004 0.041 1880 Dihedral : 5.416 52.264 1480 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 9.44 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.23), residues: 1364 helix: 2.70 (0.19), residues: 712 sheet: -1.04 (0.33), residues: 224 loop : 0.50 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 257 TYR 0.025 0.002 TYR C 213 PHE 0.015 0.002 PHE D 144 TRP 0.016 0.002 TRP A 147 HIS 0.005 0.001 HIS B 4 Details of bonding type rmsd covalent geometry : bond 0.00311 (10672) covalent geometry : angle 0.54384 (14464) hydrogen bonds : bond 0.05679 ( 571) hydrogen bonds : angle 4.40446 ( 1665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4893.70 seconds wall clock time: 84 minutes 12.05 seconds (5052.05 seconds total)