Starting phenix.real_space_refine on Sun May 3 09:28:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nt_75870/05_2026/11nt_75870.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nt_75870/05_2026/11nt_75870.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11nt_75870/05_2026/11nt_75870.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nt_75870/05_2026/11nt_75870.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11nt_75870/05_2026/11nt_75870.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nt_75870/05_2026/11nt_75870.map" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 3482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11974 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: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 361 Classifications: {'water': 361} Link IDs: {None: 360} Chain: "B" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 367 Classifications: {'water': 367} Link IDs: {None: 366} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 359 Classifications: {'water': 359} Link IDs: {None: 358} Chain: "D" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 415 Classifications: {'water': 415} Link IDs: {None: 414} Time building chain proxies: 3.50, per 1000 atoms: 0.29 Number of scatterers: 11974 At special positions: 0 Unit cell: (102.165, 81.585, 110.985, 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 3482 8.00 N 1860 7.00 C 6588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 544.7 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 8 sheets defined 54.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.857A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 46 " --> pdb=" O ARG A 42 " (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: 3.767A 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: 3.532A 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 removed outlier: 3.586A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 6.451A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 319 through 338 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 35 through 45 removed outlier: 3.830A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 258 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: 3.859A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.808A 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: 3.872A 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: 3.581A 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 302 through 314 removed outlier: 6.399A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 35 through 45 removed outlier: 4.071A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 159 through 180 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 Processing helix chain 'D' and resid 275 through 289 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: 5.928A pdb=" N GLY A 28 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 104 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ALA A 145 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE A 106 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TRP A 147 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 187 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 32 removed outlier: 6.827A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA B 32 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.806A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU C 270 " --> pdb=" O LEU C 228 " (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: 6.462A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA D 145 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLU D 187 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP D 147 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLU D 189 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS D 149 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU D 191 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU D 151 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU D 270 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 589 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.18 Time building geometry restraints manager: 1.41 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: 2137 1.33 - 1.45: 2296 1.45 - 1.57: 6183 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C PRO D 261 " pdb=" N PRO D 262 " ideal model delta sigma weight residual 1.335 1.373 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N VAL B 169 " pdb=" CA VAL B 169 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.94e+00 bond pdb=" N LYS C 146 " pdb=" CA LYS C 146 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.21e-02 6.83e+03 9.78e+00 bond pdb=" N TRP C 147 " pdb=" CA TRP C 147 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.24e-02 6.50e+03 9.40e+00 bond pdb=" CA ILE D 46 " pdb=" C ILE D 46 " ideal model delta sigma weight residual 1.523 1.562 -0.040 1.31e-02 5.83e+03 9.20e+00 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 13453 1.55 - 3.10: 839 3.10 - 4.65: 124 4.65 - 6.20: 37 6.20 - 7.75: 11 Bond angle restraints: 14464 Sorted by residual: angle pdb=" N GLN D 60 " pdb=" CA GLN D 60 " pdb=" C GLN D 60 " ideal model delta sigma weight residual 111.14 105.80 5.34 1.08e+00 8.57e-01 2.44e+01 angle pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " pdb=" CG PHE D 144 " ideal model delta sigma weight residual 113.80 118.74 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" C HIS C 4 " pdb=" CA HIS C 4 " pdb=" CB HIS C 4 " ideal model delta sigma weight residual 110.17 115.36 -5.19 1.11e+00 8.12e-01 2.19e+01 angle pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " pdb=" CG PHE B 144 " ideal model delta sigma weight residual 113.80 118.46 -4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C LYS D 288 " pdb=" CA LYS D 288 " pdb=" CB LYS D 288 " ideal model delta sigma weight residual 110.09 102.70 7.39 1.67e+00 3.59e-01 1.96e+01 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6088 17.87 - 35.75: 306 35.75 - 53.62: 62 53.62 - 71.49: 36 71.49 - 89.37: 12 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" C GLU C 278 " pdb=" N GLU C 278 " pdb=" CA GLU C 278 " pdb=" CB GLU C 278 " ideal model delta harmonic sigma weight residual -122.60 -131.21 8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C PHE D 144 " pdb=" N PHE D 144 " pdb=" CA PHE D 144 " pdb=" CB PHE D 144 " ideal model delta harmonic sigma weight residual -122.60 -131.04 8.44 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" C PHE B 144 " pdb=" N PHE B 144 " pdb=" CA PHE B 144 " pdb=" CB PHE B 144 " ideal model delta harmonic sigma weight residual -122.60 -130.85 8.25 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1271 0.057 - 0.114: 275 0.114 - 0.171: 72 0.171 - 0.229: 24 0.229 - 0.286: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA ILE D 46 " pdb=" N ILE D 46 " pdb=" C ILE D 46 " pdb=" CB ILE D 46 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA GLU B 276 " pdb=" N GLU B 276 " pdb=" C GLU B 276 " pdb=" CB GLU B 276 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LEU D 305 " pdb=" N LEU D 305 " pdb=" C LEU D 305 " pdb=" CB LEU D 305 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 292 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C LEU C 292 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU C 292 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS C 293 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 292 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C LEU A 292 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 292 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS A 293 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 213 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C TYR D 213 " 0.034 2.00e-02 2.50e+03 pdb=" O TYR D 213 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS D 214 " -0.011 2.00e-02 2.50e+03 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3539 2.81 - 3.33: 12418 3.33 - 3.86: 23488 3.86 - 4.38: 27906 4.38 - 4.90: 43445 Nonbonded interactions: 110796 Sorted by model distance: nonbonded pdb=" OH TYR A 84 " pdb=" OD2 ASP A 140 " model vdw 2.290 3.040 nonbonded pdb=" O PRO A 114 " pdb=" O HOH A 401 " model vdw 2.301 3.040 nonbonded pdb=" O HOH A 554 " pdb=" O HOH A 563 " model vdw 2.303 3.040 nonbonded pdb=" O HOH A 507 " pdb=" O HOH A 601 " model vdw 2.304 3.040 nonbonded pdb=" O MET A 232 " pdb=" O HOH A 402 " model vdw 2.306 3.040 ... (remaining 110791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.770 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.240 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 0.040 10672 Z= 0.372 Angle : 0.839 7.750 14464 Z= 0.556 Chirality : 0.057 0.286 1644 Planarity : 0.005 0.040 1880 Dihedral : 12.932 89.365 3984 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.17 % Allowed : 1.89 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.23), residues: 1364 helix: 1.19 (0.19), residues: 724 sheet: -1.33 (0.41), residues: 144 loop : 0.35 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 148 TYR 0.020 0.002 TYR D 213 PHE 0.025 0.002 PHE D 144 TRP 0.024 0.004 TRP B 313 HIS 0.007 0.001 HIS C 2 Details of bonding type rmsd covalent geometry : bond 0.00529 (10672) covalent geometry : angle 0.83893 (14464) hydrogen bonds : bond 0.14681 ( 589) hydrogen bonds : angle 6.10121 ( 1692) *********************** 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 179 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.470 Fit side-chains REVERT: A 152 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7463 (mttp) REVERT: A 292 LEU cc_start: 0.8489 (tt) cc_final: 0.8199 (tp) REVERT: A 303 ARG cc_start: 0.7476 (mtp180) cc_final: 0.6958 (ttt-90) REVERT: A 343 THR cc_start: 0.7757 (t) cc_final: 0.7543 (m) REVERT: B 13 LYS cc_start: 0.8461 (tptm) cc_final: 0.8242 (ttpp) REVERT: B 152 LYS cc_start: 0.8458 (ttmt) cc_final: 0.7990 (pttt) REVERT: B 197 ASP cc_start: 0.8748 (p0) cc_final: 0.8507 (p0) REVERT: B 237 HIS cc_start: 0.7561 (m170) cc_final: 0.7333 (m-70) REVERT: B 303 ARG cc_start: 0.6901 (ttp80) cc_final: 0.6410 (mtm-85) REVERT: B 325 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7173 (tp30) REVERT: C 13 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8320 (tppt) REVERT: C 42 ARG cc_start: 0.7042 (mmt-90) cc_final: 0.6530 (mpt180) REVERT: C 67 ASP cc_start: 0.7920 (m-30) cc_final: 0.7582 (m-30) REVERT: C 86 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7805 (mttm) REVERT: D 146 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8072 (tttt) REVERT: D 229 LYS cc_start: 0.8235 (tttt) cc_final: 0.7891 (tptm) outliers start: 13 outliers final: 5 residues processed: 177 average time/residue: 0.8993 time to fit residues: 168.2680 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 HIS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 HIS A 306 GLN B 237 HIS C 156 HIS C 168 ASN C 319 ASN D 20 HIS D 60 GLN D 136 GLN D 231 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118087 restraints weight = 11056.387| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.29 r_work: 0.3221 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10672 Z= 0.124 Angle : 0.534 6.744 14464 Z= 0.281 Chirality : 0.041 0.146 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.591 59.929 1486 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.35 % Allowed : 7.55 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 724 sheet: -1.18 (0.40), residues: 144 loop : 0.50 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.018 0.002 TYR D 213 PHE 0.015 0.002 PHE C 144 TRP 0.016 0.002 TRP A 147 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00270 (10672) covalent geometry : angle 0.53441 (14464) hydrogen bonds : bond 0.05013 ( 589) hydrogen bonds : angle 4.51894 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.493 Fit side-chains REVERT: A 52 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7164 (tp30) REVERT: A 152 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7411 (mttp) REVERT: A 292 LEU cc_start: 0.8482 (tt) cc_final: 0.8251 (tp) REVERT: A 303 ARG cc_start: 0.7499 (mtp180) cc_final: 0.6949 (ttt-90) REVERT: A 343 THR cc_start: 0.7842 (t) cc_final: 0.7548 (m) REVERT: B 13 LYS cc_start: 0.8419 (tptm) cc_final: 0.8113 (ttpp) REVERT: B 152 LYS cc_start: 0.8427 (ttmt) cc_final: 0.7947 (pttt) REVERT: B 303 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6603 (mtm-85) REVERT: B 325 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7468 (tp30) REVERT: C 13 LYS cc_start: 0.8519 (ttmm) cc_final: 0.8256 (tppt) REVERT: C 42 ARG cc_start: 0.6979 (mmt-90) cc_final: 0.6386 (mtt-85) REVERT: C 86 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7671 (mttm) REVERT: C 303 ARG cc_start: 0.7679 (ttt-90) cc_final: 0.7384 (ttt-90) REVERT: C 330 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.6900 (mmm160) REVERT: D 152 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8434 (pttp) REVERT: D 334 ASN cc_start: 0.6478 (m-40) cc_final: 0.6187 (m-40) outliers start: 15 outliers final: 9 residues processed: 115 average time/residue: 0.8498 time to fit residues: 103.9583 Evaluate side-chains 105 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 52 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 ASN C 156 HIS D 20 HIS D 231 ASN D 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.155197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115688 restraints weight = 11123.908| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.29 r_work: 0.3185 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10672 Z= 0.127 Angle : 0.526 6.195 14464 Z= 0.276 Chirality : 0.042 0.155 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.336 58.952 1480 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.71 % Allowed : 7.73 % Favored : 90.56 % 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: 2.33 (0.19), residues: 724 sheet: -1.06 (0.41), residues: 144 loop : 0.51 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 257 TYR 0.021 0.002 TYR D 213 PHE 0.013 0.002 PHE C 144 TRP 0.015 0.002 TRP A 147 HIS 0.005 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00282 (10672) covalent geometry : angle 0.52561 (14464) hydrogen bonds : bond 0.05135 ( 589) hydrogen bonds : angle 4.34428 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.465 Fit side-chains REVERT: A 139 LYS cc_start: 0.8595 (ptpp) cc_final: 0.7726 (pttp) REVERT: A 152 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7522 (mttp) REVERT: A 292 LEU cc_start: 0.8518 (tt) cc_final: 0.8289 (tp) REVERT: A 303 ARG cc_start: 0.7548 (mtp180) cc_final: 0.6927 (ttt-90) REVERT: A 343 THR cc_start: 0.7845 (t) cc_final: 0.7618 (m) REVERT: B 13 LYS cc_start: 0.8448 (tptm) cc_final: 0.8139 (ttpp) REVERT: B 45 SER cc_start: 0.8126 (m) cc_final: 0.7866 (p) REVERT: B 303 ARG cc_start: 0.7024 (ttp80) cc_final: 0.6554 (mtm-85) REVERT: B 317 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7187 (mppt) REVERT: B 325 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7488 (tp30) REVERT: C 13 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8292 (tppt) REVERT: C 42 ARG cc_start: 0.7069 (mmt-90) cc_final: 0.6384 (mtt-85) REVERT: C 86 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7710 (mttm) REVERT: C 146 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8227 (tmmt) REVERT: C 173 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.7670 (t80) REVERT: C 303 ARG cc_start: 0.7708 (ttt-90) cc_final: 0.7457 (ttt-90) REVERT: C 330 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7023 (mmm160) REVERT: D 152 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8475 (pttp) REVERT: D 334 ASN cc_start: 0.6553 (m-40) cc_final: 0.6162 (m-40) outliers start: 19 outliers final: 7 residues processed: 114 average time/residue: 0.8678 time to fit residues: 105.2091 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN C 4 HIS C 156 HIS D 231 ASN D 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114148 restraints weight = 11130.184| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.29 r_work: 0.3163 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10672 Z= 0.138 Angle : 0.539 6.062 14464 Z= 0.283 Chirality : 0.043 0.155 1644 Planarity : 0.004 0.035 1880 Dihedral : 5.404 58.040 1480 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.89 % Allowed : 8.45 % 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: 1.89 (0.23), residues: 1364 helix: 2.34 (0.19), residues: 724 sheet: -1.08 (0.40), residues: 144 loop : 0.46 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 68 TYR 0.024 0.002 TYR D 213 PHE 0.015 0.002 PHE C 144 TRP 0.014 0.002 TRP A 147 HIS 0.005 0.001 HIS C 4 Details of bonding type rmsd covalent geometry : bond 0.00311 (10672) covalent geometry : angle 0.53938 (14464) hydrogen bonds : bond 0.05394 ( 589) hydrogen bonds : angle 4.35557 ( 1692) *********************** 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 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.485 Fit side-chains REVERT: A 139 LYS cc_start: 0.8630 (ptpp) cc_final: 0.7743 (pttp) REVERT: A 152 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7555 (mttp) REVERT: A 292 LEU cc_start: 0.8520 (tt) cc_final: 0.8282 (tp) REVERT: A 303 ARG cc_start: 0.7576 (mtp180) cc_final: 0.6938 (ttt-90) REVERT: A 343 THR cc_start: 0.7867 (t) cc_final: 0.7654 (m) REVERT: B 13 LYS cc_start: 0.8462 (tptm) cc_final: 0.8148 (ttpp) REVERT: B 156 HIS cc_start: 0.7168 (m90) cc_final: 0.6575 (m90) REVERT: B 303 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6602 (mtm-85) REVERT: B 317 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7174 (mppt) REVERT: B 325 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7444 (tp30) REVERT: C 13 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8289 (tppt) REVERT: C 42 ARG cc_start: 0.7120 (mmt-90) cc_final: 0.6331 (mtt-85) REVERT: C 86 LYS cc_start: 0.8012 (mtmm) cc_final: 0.7687 (mttm) REVERT: C 146 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8285 (tmmt) REVERT: C 173 TYR cc_start: 0.9176 (OUTLIER) cc_final: 0.7668 (t80) REVERT: C 303 ARG cc_start: 0.7792 (ttt-90) cc_final: 0.7550 (ttt-90) REVERT: C 330 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7004 (mmm160) REVERT: D 334 ASN cc_start: 0.6502 (m-40) cc_final: 0.6095 (m-40) outliers start: 21 outliers final: 12 residues processed: 117 average time/residue: 0.8236 time to fit residues: 102.5958 Evaluate side-chains 117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 38 optimal weight: 0.0470 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN C 306 GLN D 231 ASN D 339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114964 restraints weight = 11065.115| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.29 r_work: 0.3176 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10672 Z= 0.127 Angle : 0.518 5.989 14464 Z= 0.272 Chirality : 0.042 0.150 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.329 57.670 1480 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.07 % Allowed : 8.63 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.23), residues: 1364 helix: 2.49 (0.19), residues: 716 sheet: -1.08 (0.40), residues: 144 loop : 0.42 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 172 TYR 0.022 0.002 TYR D 213 PHE 0.014 0.002 PHE C 144 TRP 0.012 0.001 TRP A 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00285 (10672) covalent geometry : angle 0.51827 (14464) hydrogen bonds : bond 0.05030 ( 589) hydrogen bonds : angle 4.28699 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.474 Fit side-chains REVERT: A 139 LYS cc_start: 0.8624 (ptpp) cc_final: 0.7750 (pttp) REVERT: A 152 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7546 (mttp) REVERT: A 292 LEU cc_start: 0.8523 (tt) cc_final: 0.8288 (tp) REVERT: A 303 ARG cc_start: 0.7613 (mtp180) cc_final: 0.6935 (ttt-90) REVERT: A 343 THR cc_start: 0.7905 (t) cc_final: 0.7702 (m) REVERT: B 13 LYS cc_start: 0.8433 (tptm) cc_final: 0.8137 (ttpp) REVERT: B 107 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8431 (ttmm) REVERT: B 156 HIS cc_start: 0.7123 (m90) cc_final: 0.6541 (m90) REVERT: B 303 ARG cc_start: 0.7119 (ttp80) cc_final: 0.6588 (mtm-85) REVERT: B 317 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7132 (mppt) REVERT: B 325 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7454 (tp30) REVERT: C 13 LYS cc_start: 0.8590 (ttmm) cc_final: 0.8288 (tppt) REVERT: C 42 ARG cc_start: 0.7184 (mmt-90) cc_final: 0.6369 (mtt-85) REVERT: C 86 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7704 (mttm) REVERT: C 303 ARG cc_start: 0.7782 (ttt-90) cc_final: 0.7532 (ttt-90) REVERT: C 321 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7563 (mmtm) REVERT: C 330 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7022 (mmm160) REVERT: D 152 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8392 (pttp) outliers start: 23 outliers final: 11 residues processed: 117 average time/residue: 0.8365 time to fit residues: 104.0257 Evaluate side-chains 108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN D 231 ASN D 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.155093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.115704 restraints weight = 11066.771| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.28 r_work: 0.3185 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10672 Z= 0.118 Angle : 0.502 5.842 14464 Z= 0.262 Chirality : 0.041 0.152 1644 Planarity : 0.003 0.030 1880 Dihedral : 5.255 57.820 1480 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.89 % Allowed : 9.17 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 716 sheet: -1.10 (0.40), residues: 144 loop : 0.42 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.021 0.002 TYR D 213 PHE 0.014 0.002 PHE C 144 TRP 0.012 0.001 TRP A 147 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00264 (10672) covalent geometry : angle 0.50172 (14464) hydrogen bonds : bond 0.04808 ( 589) hydrogen bonds : angle 4.21391 ( 1692) *********************** 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 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.452 Fit side-chains REVERT: A 139 LYS cc_start: 0.8582 (ptpp) cc_final: 0.7712 (pttp) REVERT: A 152 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7541 (mttp) REVERT: A 292 LEU cc_start: 0.8514 (tt) cc_final: 0.8262 (tp) REVERT: A 303 ARG cc_start: 0.7574 (mtp180) cc_final: 0.6891 (ttt-90) REVERT: B 13 LYS cc_start: 0.8421 (tptm) cc_final: 0.8128 (ttpp) REVERT: B 107 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8422 (ttmm) REVERT: B 156 HIS cc_start: 0.7087 (m90) cc_final: 0.6504 (m90) REVERT: B 303 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6584 (mtm-85) REVERT: B 317 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7141 (mppt) REVERT: B 325 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7495 (tp30) REVERT: C 13 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8275 (tppt) REVERT: C 42 ARG cc_start: 0.7218 (mmt-90) cc_final: 0.6400 (mtt180) REVERT: C 86 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7689 (mttm) REVERT: C 303 ARG cc_start: 0.7766 (ttt-90) cc_final: 0.7515 (ttt-90) REVERT: C 321 LYS cc_start: 0.8055 (mmtp) cc_final: 0.7524 (mmtm) REVERT: C 330 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7029 (mmm160) REVERT: D 152 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8393 (pttp) outliers start: 21 outliers final: 11 residues processed: 111 average time/residue: 0.8014 time to fit residues: 94.9868 Evaluate side-chains 107 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN D 231 ASN D 339 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 = 0.153460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.113742 restraints weight = 10992.377| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.28 r_work: 0.3158 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10672 Z= 0.142 Angle : 0.536 5.707 14464 Z= 0.282 Chirality : 0.042 0.153 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.392 57.407 1480 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.98 % Allowed : 9.17 % Favored : 88.85 % 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: 2.45 (0.19), residues: 716 sheet: -1.12 (0.40), residues: 144 loop : 0.36 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.026 0.002 TYR D 213 PHE 0.016 0.002 PHE C 144 TRP 0.013 0.002 TRP A 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00321 (10672) covalent geometry : angle 0.53633 (14464) hydrogen bonds : bond 0.05422 ( 589) hydrogen bonds : angle 4.32131 ( 1692) *********************** 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 116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.461 Fit side-chains REVERT: A 139 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.7752 (pttp) REVERT: A 152 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7588 (mttp) REVERT: A 292 LEU cc_start: 0.8518 (tt) cc_final: 0.8271 (tp) REVERT: A 303 ARG cc_start: 0.7650 (mtp180) cc_final: 0.6950 (ttt-90) REVERT: B 13 LYS cc_start: 0.8464 (tptm) cc_final: 0.8180 (ttpp) REVERT: B 107 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8443 (ttmm) REVERT: B 156 HIS cc_start: 0.7122 (m90) cc_final: 0.6528 (m90) REVERT: B 303 ARG cc_start: 0.7134 (ttp80) cc_final: 0.6615 (mtm-85) REVERT: B 325 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7469 (tp30) REVERT: C 13 LYS cc_start: 0.8620 (ttmm) cc_final: 0.8313 (tppt) REVERT: C 42 ARG cc_start: 0.7219 (mmt-90) cc_final: 0.6408 (mtt180) REVERT: C 86 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7735 (mttt) REVERT: C 303 ARG cc_start: 0.7775 (ttt-90) cc_final: 0.7537 (ttt-90) REVERT: C 321 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7534 (mmtm) REVERT: C 330 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.7085 (mmm160) outliers start: 22 outliers final: 13 residues processed: 109 average time/residue: 0.8487 time to fit residues: 98.3408 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN C 319 ASN D 231 ASN D 339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112884 restraints weight = 10972.984| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.28 r_work: 0.3145 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10672 Z= 0.155 Angle : 0.557 5.860 14464 Z= 0.293 Chirality : 0.043 0.158 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.476 57.028 1480 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 9.17 % Favored : 88.94 % 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: 1.66 (0.23), residues: 1364 helix: 2.28 (0.19), residues: 724 sheet: -1.60 (0.37), residues: 176 loop : 0.45 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 172 TYR 0.027 0.002 TYR D 213 PHE 0.016 0.002 PHE C 144 TRP 0.013 0.002 TRP A 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00354 (10672) covalent geometry : angle 0.55677 (14464) hydrogen bonds : bond 0.05692 ( 589) hydrogen bonds : angle 4.38131 ( 1692) *********************** 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 116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.488 Fit side-chains REVERT: A 139 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: A 152 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7592 (mttp) REVERT: A 292 LEU cc_start: 0.8529 (tt) cc_final: 0.8284 (tp) REVERT: A 303 ARG cc_start: 0.7715 (mtp180) cc_final: 0.6973 (ttt-90) REVERT: B 13 LYS cc_start: 0.8484 (tptm) cc_final: 0.8157 (ttpp) REVERT: B 107 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8453 (ttmm) REVERT: B 156 HIS cc_start: 0.7133 (m90) cc_final: 0.6534 (m90) REVERT: B 303 ARG cc_start: 0.7156 (ttp80) cc_final: 0.6637 (mtm-85) REVERT: B 325 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7446 (tp30) REVERT: C 13 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8323 (tppt) REVERT: C 42 ARG cc_start: 0.7221 (mmt-90) cc_final: 0.6360 (mtt180) REVERT: C 86 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7770 (mttt) REVERT: C 173 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8054 (t80) REVERT: C 303 ARG cc_start: 0.7768 (ttt-90) cc_final: 0.7559 (ttt-90) REVERT: C 321 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7516 (mmtm) REVERT: C 330 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7095 (mmm160) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.8421 time to fit residues: 99.5938 Evaluate side-chains 109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 38 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN D 20 HIS D 231 ASN D 339 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113294 restraints weight = 10925.280| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.27 r_work: 0.3151 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10672 Z= 0.147 Angle : 0.545 5.880 14464 Z= 0.287 Chirality : 0.043 0.156 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.450 56.911 1480 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.89 % Allowed : 9.44 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.23), residues: 1364 helix: 2.28 (0.19), residues: 724 sheet: -1.17 (0.40), residues: 144 loop : 0.36 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.026 0.002 TYR D 213 PHE 0.015 0.002 PHE C 144 TRP 0.013 0.002 TRP A 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00336 (10672) covalent geometry : angle 0.54534 (14464) hydrogen bonds : bond 0.05497 ( 589) hydrogen bonds : angle 4.35032 ( 1692) *********************** 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 115 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.494 Fit side-chains REVERT: A 139 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8402 (ptpp) REVERT: A 152 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7571 (mttp) REVERT: A 292 LEU cc_start: 0.8531 (tt) cc_final: 0.8286 (tp) REVERT: A 303 ARG cc_start: 0.7711 (mtp180) cc_final: 0.6976 (ttt-90) REVERT: B 13 LYS cc_start: 0.8468 (tptm) cc_final: 0.8158 (ttpp) REVERT: B 107 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8435 (ttmm) REVERT: B 156 HIS cc_start: 0.7122 (m90) cc_final: 0.6530 (m90) REVERT: B 303 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6667 (mtm-85) REVERT: B 325 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7438 (tp30) REVERT: C 13 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8312 (tppt) REVERT: C 42 ARG cc_start: 0.7261 (mmt-90) cc_final: 0.6364 (mtt180) REVERT: C 86 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7808 (mttt) REVERT: C 173 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.7962 (t80) REVERT: C 303 ARG cc_start: 0.7760 (ttt-90) cc_final: 0.7558 (ttt-90) REVERT: C 321 LYS cc_start: 0.8038 (mmtp) cc_final: 0.7495 (mmtm) REVERT: C 330 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7083 (mmm160) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.8585 time to fit residues: 101.3091 Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP 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 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.1980 chunk 7 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN D 231 ASN D 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115067 restraints weight = 11076.856| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.28 r_work: 0.3178 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10672 Z= 0.120 Angle : 0.510 5.865 14464 Z= 0.267 Chirality : 0.041 0.150 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.303 57.450 1480 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.71 % Allowed : 9.53 % Favored : 88.76 % 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: 2.41 (0.19), residues: 724 sheet: -1.15 (0.40), residues: 144 loop : 0.41 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.021 0.002 TYR D 213 PHE 0.014 0.002 PHE C 144 TRP 0.012 0.001 TRP A 147 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00270 (10672) covalent geometry : angle 0.50996 (14464) hydrogen bonds : bond 0.04886 ( 589) hydrogen bonds : angle 4.23635 ( 1692) ********************** 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 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.460 Fit side-chains REVERT: A 139 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.7774 (pttp) REVERT: A 152 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7547 (mttp) REVERT: A 292 LEU cc_start: 0.8518 (tt) cc_final: 0.8266 (tp) REVERT: A 303 ARG cc_start: 0.7667 (mtp180) cc_final: 0.6949 (ttt-90) REVERT: B 13 LYS cc_start: 0.8425 (tptm) cc_final: 0.8135 (ttpp) REVERT: B 107 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8417 (ttmm) REVERT: B 156 HIS cc_start: 0.7080 (m90) cc_final: 0.6487 (m90) REVERT: B 303 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6633 (mtm-85) REVERT: B 325 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7418 (tp30) REVERT: C 13 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8327 (tmtm) REVERT: C 42 ARG cc_start: 0.7290 (mmt-90) cc_final: 0.6420 (mtt180) REVERT: C 86 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7798 (mttt) REVERT: C 303 ARG cc_start: 0.7756 (ttt-90) cc_final: 0.7555 (ttt-90) REVERT: C 330 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7026 (mmm160) REVERT: D 152 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8390 (pttp) outliers start: 19 outliers final: 12 residues processed: 109 average time/residue: 0.8321 time to fit residues: 96.5479 Evaluate side-chains 111 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 295 TRP Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 237 HIS Chi-restraints excluded: chain B residue 295 TRP Chi-restraints excluded: chain C residue 38 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 330 ARG Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 295 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN D 231 ASN D 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.153351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.113842 restraints weight = 11050.583| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.28 r_work: 0.3160 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10672 Z= 0.139 Angle : 0.535 5.763 14464 Z= 0.281 Chirality : 0.042 0.152 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.389 57.231 1480 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.62 % Allowed : 9.71 % Favored : 88.67 % 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: 1.83 (0.23), residues: 1364 helix: 2.35 (0.19), residues: 724 sheet: -1.15 (0.40), residues: 144 loop : 0.36 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.025 0.002 TYR D 213 PHE 0.015 0.002 PHE C 144 TRP 0.012 0.002 TRP A 147 HIS 0.004 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00316 (10672) covalent geometry : angle 0.53452 (14464) hydrogen bonds : bond 0.05339 ( 589) hydrogen bonds : angle 4.30300 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5198.48 seconds wall clock time: 89 minutes 22.81 seconds (5362.81 seconds total)