Starting phenix.real_space_refine on Sat Aug 23 07:49:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twl_41670/08_2025/8twl_41670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twl_41670/08_2025/8twl_41670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8twl_41670/08_2025/8twl_41670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twl_41670/08_2025/8twl_41670.map" model { file = "/net/cci-nas-00/data/ceres_data/8twl_41670/08_2025/8twl_41670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twl_41670/08_2025/8twl_41670.cif" } resolution = 2.7 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= -0.001 sd= 0.066 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 2308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10800 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "C" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Time building chain proxies: 2.63, per 1000 atoms: 0.24 Number of scatterers: 10800 At special positions: 0 Unit cell: (103.53, 79.17, 96.57, 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 2308 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: 0.60 Conformation dependent library (CDL) restraints added in 358.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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 54.3% alpha, 12.4% 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 37 through 45 removed outlier: 3.641A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 4.105A 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 81 through 85 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 159 through 180 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 302 through 314 removed outlier: 3.655A pdb=" N GLN A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 5.058A 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 339 Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 37 through 45 removed outlier: 3.630A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 197 through 219 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 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 339 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 37 through 45 removed outlier: 3.611A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 66 through 70 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 159 through 180 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: 3.614A pdb=" N GLN C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.056A 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 339 Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 37 through 45 removed outlier: 3.780A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 4.104A 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 71 Proline residue: D 71 - end of helix 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 288 Processing helix chain 'D' and resid 302 through 314 removed outlier: 3.538A pdb=" N GLN D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N SER D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA D 309 " --> pdb=" O LEU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 318 No H-bonds generated for 'chain 'D' and resid 316 through 318' Processing helix chain 'D' and resid 319 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.451A pdb=" N GLY A 28 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A 76 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 30 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU A 78 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY A 74 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLY A 105 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 76 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LYS A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU A 78 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 104 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS A 146 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 106 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ARG A 148 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP A 147 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 228 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 267 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER A 300 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE A 269 " --> pdb=" O SER A 300 " (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: 6.432A pdb=" N GLY B 28 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL B 76 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 30 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU B 78 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY B 74 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLY B 105 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS B 107 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU B 78 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 104 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LYS B 146 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 106 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ARG B 148 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 147 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 187 " --> pdb=" O TRP B 147 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU B 228 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL B 267 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER B 300 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE B 269 " --> pdb=" O SER B 300 " (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: 6.464A pdb=" N GLY C 28 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL C 76 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU C 30 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU C 78 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY C 74 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY C 105 " --> pdb=" O GLY C 74 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 104 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYS C 146 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE C 106 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ARG C 148 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TRP C 147 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C 228 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL C 267 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER C 300 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N PHE C 269 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA7, first strand: chain 'D' and resid 28 through 32 removed outlier: 6.445A pdb=" N GLY D 28 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL D 76 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 30 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU D 78 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA D 32 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY D 74 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLY D 105 " --> pdb=" O GLY D 74 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D 104 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS D 146 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 106 " --> pdb=" O LYS D 146 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ARG D 148 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP D 147 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU D 228 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL D 267 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER D 300 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE D 269 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 112 through 114 554 hydrogen bonds defined for protein. 1590 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: 1.51 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3516 1.34 - 1.46: 2029 1.46 - 1.58: 5071 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" CB PRO A 5 " pdb=" CG PRO A 5 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 6.99e-01 bond pdb=" CB PRO B 158 " pdb=" CG PRO B 158 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.94e-01 bond pdb=" CB PRO A 158 " pdb=" CG PRO A 158 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.74e-01 bond pdb=" CB PRO D 158 " pdb=" CG PRO D 158 " ideal model delta sigma weight residual 1.506 1.474 0.032 3.90e-02 6.57e+02 6.59e-01 bond pdb=" CB PRO B 5 " pdb=" CG PRO B 5 " ideal model delta sigma weight residual 1.492 1.532 -0.040 5.00e-02 4.00e+02 6.54e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 14120 1.31 - 2.62: 265 2.62 - 3.93: 58 3.93 - 5.24: 13 5.24 - 6.55: 8 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA LEU C 320 " pdb=" CB LEU C 320 " pdb=" CG LEU C 320 " ideal model delta sigma weight residual 116.30 122.85 -6.55 3.50e+00 8.16e-02 3.50e+00 angle pdb=" CA LEU B 61 " pdb=" CB LEU B 61 " pdb=" CG LEU B 61 " ideal model delta sigma weight residual 116.30 122.82 -6.52 3.50e+00 8.16e-02 3.47e+00 angle pdb=" CA LEU D 320 " pdb=" CB LEU D 320 " pdb=" CG LEU D 320 " ideal model delta sigma weight residual 116.30 122.54 -6.24 3.50e+00 8.16e-02 3.18e+00 angle pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sigma weight residual 116.30 122.47 -6.17 3.50e+00 8.16e-02 3.11e+00 angle pdb=" CA TYR B 213 " pdb=" CB TYR B 213 " pdb=" CG TYR B 213 " ideal model delta sigma weight residual 113.90 110.74 3.16 1.80e+00 3.09e-01 3.07e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5655 16.89 - 33.79: 577 33.79 - 50.68: 191 50.68 - 67.58: 60 67.58 - 84.47: 21 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CG ARG A 59 " pdb=" CD ARG A 59 " pdb=" NE ARG A 59 " pdb=" CZ ARG A 59 " ideal model delta sinusoidal sigma weight residual -90.00 -134.99 44.99 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG B 59 " pdb=" CD ARG B 59 " pdb=" NE ARG B 59 " pdb=" CZ ARG B 59 " ideal model delta sinusoidal sigma weight residual -90.00 -134.96 44.96 2 1.50e+01 4.44e-03 1.07e+01 dihedral pdb=" CG ARG C 59 " pdb=" CD ARG C 59 " pdb=" NE ARG C 59 " pdb=" CZ ARG C 59 " ideal model delta sinusoidal sigma weight residual -180.00 -135.61 -44.39 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 933 0.024 - 0.047: 387 0.047 - 0.071: 167 0.071 - 0.094: 102 0.094 - 0.118: 55 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA ILE C 77 " pdb=" N ILE C 77 " pdb=" C ILE C 77 " pdb=" CB ILE C 77 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE A 77 " pdb=" N ILE A 77 " pdb=" C ILE A 77 " pdb=" CB ILE A 77 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 4 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 5 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 4 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO B 5 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 5 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 5 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 4 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO D 5 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 5 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 5 " -0.022 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 539 2.70 - 3.25: 11198 3.25 - 3.80: 21253 3.80 - 4.35: 27620 4.35 - 4.90: 43526 Nonbonded interactions: 104136 Sorted by model distance: nonbonded pdb=" OG SER D 308 " pdb=" OE1 GLU D 326 " model vdw 2.155 3.040 nonbonded pdb=" NZ LYS C 207 " pdb=" O SER D 217 " model vdw 2.204 3.120 nonbonded pdb=" NZ LYS A 207 " pdb=" O SER B 217 " model vdw 2.204 3.120 nonbonded pdb=" O MET C 250 " pdb=" OG1 THR C 254 " model vdw 2.206 3.040 nonbonded pdb=" O SER A 217 " pdb=" NZ LYS B 207 " model vdw 2.209 3.120 ... (remaining 104131 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: 1.060 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.003 0.042 10672 Z= 0.129 Angle : 0.502 6.551 14464 Z= 0.254 Chirality : 0.038 0.118 1644 Planarity : 0.004 0.044 1880 Dihedral : 16.845 84.469 3984 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.34 % Allowed : 18.26 % Favored : 79.41 % 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 aren not related in a simple way. whole: 1.43 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 716 sheet: -1.53 (0.35), residues: 184 loop : 0.29 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 200 TYR 0.011 0.001 TYR B 213 PHE 0.011 0.001 PHE A 144 TRP 0.011 0.002 TRP B 147 HIS 0.002 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00307 (10672) covalent geometry : angle 0.50231 (14464) hydrogen bonds : bond 0.13896 ( 554) hydrogen bonds : angle 5.45607 ( 1590) *********************** 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 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.292 Fit side-chains REVERT: C 321 LYS cc_start: 0.7425 (tttm) cc_final: 0.7163 (tptt) outliers start: 26 outliers final: 22 residues processed: 125 average time/residue: 0.6114 time to fit residues: 81.5466 Evaluate side-chains 118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 270 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 241 GLN B 166 ASN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 ASN C 241 GLN D 166 ASN D 241 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120332 restraints weight = 10584.565| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.31 r_work: 0.3224 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10672 Z= 0.145 Angle : 0.533 7.495 14464 Z= 0.268 Chirality : 0.041 0.151 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.644 47.284 1508 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.15 % Allowed : 14.84 % Favored : 82.01 % 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 aren not related in a simple way. whole: 1.46 (0.23), residues: 1364 helix: 2.26 (0.19), residues: 720 sheet: -1.81 (0.30), residues: 216 loop : 0.42 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.014 0.002 TYR B 213 PHE 0.013 0.002 PHE D 144 TRP 0.012 0.002 TRP B 147 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00337 (10672) covalent geometry : angle 0.53259 (14464) hydrogen bonds : bond 0.03868 ( 554) hydrogen bonds : angle 4.51289 ( 1590) *********************** 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 141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.521 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 124 average time/residue: 0.8534 time to fit residues: 112.1451 Evaluate side-chains 113 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 59 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 168 ASN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN B 324 GLN C 168 ASN C 241 GLN C 319 ASN D 241 GLN D 319 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119040 restraints weight = 10815.488| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.33 r_work: 0.3222 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.134 Angle : 0.508 7.167 14464 Z= 0.254 Chirality : 0.040 0.137 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.145 48.028 1488 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.69 % Allowed : 13.85 % Favored : 82.46 % 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 aren not related in a simple way. whole: 1.50 (0.23), residues: 1364 helix: 2.31 (0.19), residues: 720 sheet: -1.88 (0.31), residues: 216 loop : 0.43 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.013 0.001 TYR C 213 PHE 0.013 0.002 PHE C 144 TRP 0.012 0.002 TRP B 147 HIS 0.003 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00316 (10672) covalent geometry : angle 0.50816 (14464) hydrogen bonds : bond 0.03570 ( 554) hydrogen bonds : angle 4.31764 ( 1590) *********************** 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 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.453 Fit side-chains REVERT: A 107 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8263 (ttmm) REVERT: A 326 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.7006 (mm-30) REVERT: B 303 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5140 (mtp-110) outliers start: 41 outliers final: 31 residues processed: 132 average time/residue: 0.7148 time to fit residues: 100.9085 Evaluate side-chains 116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 0.0170 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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 ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121744 restraints weight = 10734.520| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.21 r_work: 0.3207 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10672 Z= 0.151 Angle : 0.519 6.971 14464 Z= 0.260 Chirality : 0.040 0.138 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.237 53.868 1488 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.05 % Allowed : 13.31 % Favored : 82.64 % 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 aren not related in a simple way. whole: 1.44 (0.23), residues: 1364 helix: 2.27 (0.19), residues: 720 sheet: -1.93 (0.30), residues: 216 loop : 0.40 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.015 0.001 TYR B 213 PHE 0.014 0.002 PHE C 144 TRP 0.013 0.002 TRP B 147 HIS 0.003 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00362 (10672) covalent geometry : angle 0.51927 (14464) hydrogen bonds : bond 0.03569 ( 554) hydrogen bonds : angle 4.27400 ( 1590) *********************** 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 145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.436 Fit side-chains REVERT: A 107 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8306 (ttmm) REVERT: A 321 LYS cc_start: 0.6677 (mmtm) cc_final: 0.5671 (tptt) REVERT: B 303 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5225 (mtp-110) REVERT: B 325 GLU cc_start: 0.7295 (tp30) cc_final: 0.7062 (mm-30) REVERT: C 325 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7202 (mm-30) REVERT: D 86 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7256 (mttp) outliers start: 45 outliers final: 32 residues processed: 135 average time/residue: 0.7134 time to fit residues: 102.9830 Evaluate side-chains 125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 0.0980 chunk 123 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120677 restraints weight = 10674.467| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.31 r_work: 0.3209 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.134 Angle : 0.504 6.847 14464 Z= 0.252 Chirality : 0.040 0.134 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.165 58.121 1486 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.05 % Allowed : 13.58 % Favored : 82.37 % 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 aren not related in a simple way. whole: 1.51 (0.23), residues: 1364 helix: 2.35 (0.19), residues: 720 sheet: -1.94 (0.30), residues: 216 loop : 0.44 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.014 0.001 TYR B 213 PHE 0.013 0.002 PHE C 144 TRP 0.012 0.002 TRP B 147 HIS 0.002 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00319 (10672) covalent geometry : angle 0.50436 (14464) hydrogen bonds : bond 0.03378 ( 554) hydrogen bonds : angle 4.20107 ( 1590) *********************** 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 140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.411 Fit side-chains REVERT: A 107 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8250 (ttmm) REVERT: A 321 LYS cc_start: 0.6615 (mmtm) cc_final: 0.5574 (tptt) REVERT: B 303 ARG cc_start: 0.6163 (OUTLIER) cc_final: 0.5048 (mtp-110) REVERT: B 325 GLU cc_start: 0.7221 (tp30) cc_final: 0.6940 (mm-30) REVERT: C 325 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6774 (mm-30) REVERT: D 86 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7152 (mttp) outliers start: 45 outliers final: 39 residues processed: 128 average time/residue: 0.6739 time to fit residues: 92.5187 Evaluate side-chains 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 86 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120618 restraints weight = 10699.593| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.26 r_work: 0.3211 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10672 Z= 0.147 Angle : 0.512 6.902 14464 Z= 0.256 Chirality : 0.040 0.135 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.172 55.267 1486 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.23 % Allowed : 13.67 % Favored : 82.10 % 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 aren not related in a simple way. whole: 1.48 (0.23), residues: 1364 helix: 2.31 (0.19), residues: 720 sheet: -1.93 (0.30), residues: 216 loop : 0.44 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.014 0.001 TYR A 213 PHE 0.013 0.002 PHE C 144 TRP 0.013 0.002 TRP B 147 HIS 0.003 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00351 (10672) covalent geometry : angle 0.51241 (14464) hydrogen bonds : bond 0.03453 ( 554) hydrogen bonds : angle 4.21070 ( 1590) *********************** 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 141 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 0.448 Fit side-chains REVERT: A 107 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8264 (ttmm) REVERT: A 193 ASP cc_start: 0.8062 (m-30) cc_final: 0.7746 (m-30) REVERT: A 321 LYS cc_start: 0.6620 (mmtm) cc_final: 0.5564 (tptt) REVERT: B 303 ARG cc_start: 0.6218 (OUTLIER) cc_final: 0.5022 (mtp-110) REVERT: B 325 GLU cc_start: 0.7249 (tp30) cc_final: 0.6957 (mm-30) REVERT: C 325 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: D 86 LYS cc_start: 0.7810 (mtpt) cc_final: 0.7185 (mttp) outliers start: 47 outliers final: 36 residues processed: 130 average time/residue: 0.6968 time to fit residues: 97.0627 Evaluate side-chains 124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 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 ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121419 restraints weight = 10711.129| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.26 r_work: 0.3257 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10672 Z= 0.136 Angle : 0.504 6.835 14464 Z= 0.252 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.078 57.278 1484 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.05 % Allowed : 13.76 % Favored : 82.19 % 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 aren not related in a simple way. whole: 1.51 (0.23), residues: 1364 helix: 2.34 (0.19), residues: 720 sheet: -1.94 (0.30), residues: 216 loop : 0.44 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.013 0.001 TYR C 213 PHE 0.013 0.002 PHE C 144 TRP 0.012 0.002 TRP B 147 HIS 0.002 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00325 (10672) covalent geometry : angle 0.50371 (14464) hydrogen bonds : bond 0.03359 ( 554) hydrogen bonds : angle 4.17282 ( 1590) *********************** 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 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 94 time to evaluate : 0.357 Fit side-chains REVERT: A 107 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8282 (ttmm) REVERT: A 193 ASP cc_start: 0.8089 (m-30) cc_final: 0.7765 (m-30) REVERT: A 321 LYS cc_start: 0.6692 (mmtm) cc_final: 0.5760 (tptt) REVERT: B 303 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5132 (mtp-110) REVERT: B 325 GLU cc_start: 0.7334 (tp30) cc_final: 0.7097 (mm-30) REVERT: C 325 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: D 86 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7325 (mttp) outliers start: 45 outliers final: 38 residues processed: 127 average time/residue: 0.6969 time to fit residues: 94.6982 Evaluate side-chains 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 82 optimal weight: 0.2980 chunk 112 optimal weight: 0.0670 chunk 127 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125057 restraints weight = 10639.552| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.21 r_work: 0.3261 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10672 Z= 0.116 Angle : 0.488 6.840 14464 Z= 0.243 Chirality : 0.039 0.130 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.911 53.056 1484 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.69 % Allowed : 14.48 % Favored : 81.83 % 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 aren not related in a simple way. whole: 1.60 (0.23), residues: 1364 helix: 2.43 (0.19), residues: 720 sheet: -1.93 (0.31), residues: 216 loop : 0.47 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.011 0.001 TYR C 213 PHE 0.012 0.001 PHE D 144 TRP 0.011 0.002 TRP C 147 HIS 0.002 0.000 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00273 (10672) covalent geometry : angle 0.48813 (14464) hydrogen bonds : bond 0.03168 ( 554) hydrogen bonds : angle 4.10005 ( 1590) *********************** 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 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 96 time to evaluate : 0.460 Fit side-chains REVERT: A 107 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8200 (ttmm) REVERT: A 164 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8409 (tmm) REVERT: A 321 LYS cc_start: 0.6776 (mmtm) cc_final: 0.5741 (tptt) REVERT: B 303 ARG cc_start: 0.6232 (OUTLIER) cc_final: 0.5063 (mtp-110) REVERT: B 325 GLU cc_start: 0.7263 (tp30) cc_final: 0.7023 (mm-30) REVERT: C 325 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: D 86 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7240 (mttp) REVERT: D 164 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8399 (tmm) outliers start: 41 outliers final: 31 residues processed: 123 average time/residue: 0.6664 time to fit residues: 88.1364 Evaluate side-chains 123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 83 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.122911 restraints weight = 10738.214| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.23 r_work: 0.3234 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.126 Angle : 0.495 6.871 14464 Z= 0.247 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.032 1880 Dihedral : 4.887 48.165 1484 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.33 % Allowed : 15.02 % Favored : 81.65 % 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 aren not related in a simple way. whole: 1.60 (0.23), residues: 1364 helix: 2.41 (0.19), residues: 720 sheet: -1.91 (0.31), residues: 216 loop : 0.49 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.012 0.001 TYR C 213 PHE 0.013 0.001 PHE B 144 TRP 0.012 0.002 TRP C 147 HIS 0.002 0.000 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00301 (10672) covalent geometry : angle 0.49524 (14464) hydrogen bonds : bond 0.03233 ( 554) hydrogen bonds : angle 4.10751 ( 1590) *********************** 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 132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.462 Fit side-chains REVERT: A 107 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8252 (ttmm) REVERT: A 164 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8425 (tmm) REVERT: A 321 LYS cc_start: 0.6787 (mmtm) cc_final: 0.5761 (tptt) REVERT: B 303 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5041 (mtp-110) REVERT: B 325 GLU cc_start: 0.7281 (tp30) cc_final: 0.7037 (mm-30) REVERT: C 86 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7151 (mtmt) REVERT: C 325 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: D 86 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7281 (mttp) REVERT: D 164 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8411 (tmm) outliers start: 37 outliers final: 30 residues processed: 122 average time/residue: 0.6669 time to fit residues: 87.6394 Evaluate side-chains 125 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.146240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124161 restraints weight = 10676.020| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.21 r_work: 0.3250 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.125 Angle : 0.494 6.863 14464 Z= 0.246 Chirality : 0.040 0.132 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.834 47.130 1484 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.42 % Allowed : 14.93 % Favored : 81.65 % 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 aren not related in a simple way. whole: 1.61 (0.23), residues: 1364 helix: 2.42 (0.19), residues: 720 sheet: -1.92 (0.31), residues: 216 loop : 0.50 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.012 0.001 TYR C 213 PHE 0.013 0.001 PHE A 144 TRP 0.012 0.002 TRP C 147 HIS 0.002 0.000 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00297 (10672) covalent geometry : angle 0.49416 (14464) hydrogen bonds : bond 0.03197 ( 554) hydrogen bonds : angle 4.09826 ( 1590) ********************** 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 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 0.539 Fit side-chains REVERT: A 107 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8251 (ttmm) REVERT: A 164 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: A 321 LYS cc_start: 0.6797 (mmtm) cc_final: 0.5786 (tptt) REVERT: B 303 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5035 (mtp-110) REVERT: B 325 GLU cc_start: 0.7297 (tp30) cc_final: 0.7053 (mm-30) REVERT: C 86 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7176 (mtmt) REVERT: C 325 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6728 (mm-30) REVERT: D 100 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7347 (tttp) REVERT: D 164 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8429 (tmm) outliers start: 38 outliers final: 31 residues processed: 119 average time/residue: 0.6769 time to fit residues: 86.4985 Evaluate side-chains 122 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 45 optimal weight: 0.0270 chunk 73 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.145781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122804 restraints weight = 10734.520| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.27 r_work: 0.3267 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.121 Angle : 0.491 6.849 14464 Z= 0.245 Chirality : 0.040 0.131 1644 Planarity : 0.004 0.033 1880 Dihedral : 4.782 47.125 1484 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.51 % Allowed : 14.66 % Favored : 81.83 % 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 aren not related in a simple way. whole: 1.64 (0.24), residues: 1364 helix: 2.44 (0.19), residues: 720 sheet: -1.89 (0.31), residues: 216 loop : 0.52 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.012 0.001 TYR C 213 PHE 0.012 0.001 PHE A 144 TRP 0.012 0.002 TRP C 147 HIS 0.002 0.000 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00287 (10672) covalent geometry : angle 0.49136 (14464) hydrogen bonds : bond 0.03161 ( 554) hydrogen bonds : angle 4.07910 ( 1590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3534.47 seconds wall clock time: 61 minutes 34.43 seconds (3694.43 seconds total)