Starting phenix.real_space_refine on Mon Jul 28 20:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twl_41670/07_2025/8twl_41670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twl_41670/07_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_41670/07_2025/8twl_41670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twl_41670/07_2025/8twl_41670.map" model { file = "/net/cci-nas-00/data/ceres_data/8twl_41670/07_2025/8twl_41670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twl_41670/07_2025/8twl_41670.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.47, per 1000 atoms: 0.69 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: 2.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.27 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: 3.62 Time building geometry restraints manager: 3.41 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: 0.03 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.060 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 43.550 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.002 TRP B 147 HIS 0.002 0.001 HIS D 80 PHE 0.011 0.001 PHE A 144 TYR 0.011 0.001 TYR B 213 ARG 0.004 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.13896 ( 554) hydrogen bonds : angle 5.45607 ( 1590) covalent geometry : bond 0.00307 (10672) covalent geometry : angle 0.50231 (14464) *********************** 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 : 1.219 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: 1.4305 time to fit residues: 191.6176 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 : 1.251 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.0170 chunk 35 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.142463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118713 restraints weight = 10616.828| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.26 r_work: 0.3218 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10672 Z= 0.151 Angle : 0.537 7.550 14464 Z= 0.270 Chirality : 0.041 0.148 1644 Planarity : 0.004 0.029 1880 Dihedral : 5.676 47.163 1508 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.15 % Allowed : 15.11 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.23), residues: 1364 helix: 2.25 (0.19), residues: 720 sheet: -1.81 (0.30), residues: 216 loop : 0.43 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 147 HIS 0.003 0.001 HIS A 80 PHE 0.013 0.002 PHE D 144 TYR 0.015 0.002 TYR B 213 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 554) hydrogen bonds : angle 4.55576 ( 1590) covalent geometry : bond 0.00348 (10672) covalent geometry : angle 0.53654 (14464) *********************** 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 : 1.123 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 124 average time/residue: 1.6254 time to fit residues: 214.4719 Evaluate side-chains 116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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 311 LYS 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 7 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 136 GLN C 168 ASN C 241 GLN C 319 ASN D 166 ASN D 241 GLN D 319 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.112417 restraints weight = 10755.459| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.35 r_work: 0.3129 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10672 Z= 0.215 Angle : 0.578 7.220 14464 Z= 0.293 Chirality : 0.043 0.145 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.478 53.090 1488 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.23), residues: 1364 helix: 2.02 (0.19), residues: 720 sheet: -1.94 (0.30), residues: 216 loop : 0.30 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 147 HIS 0.005 0.001 HIS D 80 PHE 0.017 0.002 PHE C 144 TYR 0.019 0.002 TYR D 213 ARG 0.003 0.001 ARG C 330 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 554) hydrogen bonds : angle 4.49449 ( 1590) covalent geometry : bond 0.00516 (10672) covalent geometry : angle 0.57806 (14464) *********************** 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 157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 1.133 Fit side-chains REVERT: A 107 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8392 (ttmm) REVERT: A 247 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8352 (mt-10) REVERT: A 321 LYS cc_start: 0.6748 (mmtm) cc_final: 0.5728 (tptt) REVERT: B 152 LYS cc_start: 0.8225 (pttp) cc_final: 0.8013 (pttp) REVERT: B 325 GLU cc_start: 0.7328 (tp30) cc_final: 0.7093 (mm-30) REVERT: C 247 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8383 (mt-10) REVERT: C 321 LYS cc_start: 0.7539 (tttm) cc_final: 0.7296 (tptt) REVERT: D 86 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7319 (mttp) REVERT: D 321 LYS cc_start: 0.6799 (mmtm) cc_final: 0.5766 (tptt) outliers start: 45 outliers final: 32 residues processed: 145 average time/residue: 1.4305 time to fit residues: 222.2638 Evaluate side-chains 129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 247 GLU 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 212 VAL Chi-restraints excluded: chain B residue 270 LEU 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 247 GLU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 320 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 134 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 102 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.3596 r_free = 0.3596 target = 0.141843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119521 restraints weight = 10648.328| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.20 r_work: 0.3204 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1275 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= 0.140 Angle : 0.517 7.060 14464 Z= 0.260 Chirality : 0.040 0.137 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.338 56.641 1488 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.69 % Allowed : 14.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1364 helix: 2.20 (0.19), residues: 720 sheet: -2.01 (0.30), residues: 216 loop : 0.40 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.003 0.000 HIS D 80 PHE 0.013 0.002 PHE C 144 TYR 0.015 0.001 TYR C 213 ARG 0.003 0.000 ARG D 172 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 554) hydrogen bonds : angle 4.32743 ( 1590) covalent geometry : bond 0.00333 (10672) covalent geometry : angle 0.51673 (14464) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 1.194 Fit side-chains REVERT: A 107 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8320 (ttmm) REVERT: A 295 TRP cc_start: 0.8867 (OUTLIER) cc_final: 0.7322 (m-90) REVERT: B 295 TRP cc_start: 0.8891 (OUTLIER) cc_final: 0.7328 (m-90) REVERT: B 325 GLU cc_start: 0.7273 (tp30) cc_final: 0.7030 (mm-30) REVERT: C 295 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.7431 (m-90) REVERT: C 325 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: D 86 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7286 (mttp) outliers start: 41 outliers final: 33 residues processed: 120 average time/residue: 1.3906 time to fit residues: 179.5173 Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 83 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 295 TRP 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 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 295 TRP 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 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain 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 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3576 r_free = 0.3576 target = 0.140722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115573 restraints weight = 10622.855| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.36 r_work: 0.3161 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10672 Z= 0.137 Angle : 0.508 6.867 14464 Z= 0.254 Chirality : 0.040 0.135 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.307 58.430 1488 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.60 % Allowed : 14.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.23), residues: 1364 helix: 2.27 (0.19), residues: 720 sheet: -1.98 (0.30), residues: 216 loop : 0.41 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 295 HIS 0.002 0.001 HIS D 80 PHE 0.013 0.002 PHE C 144 TYR 0.014 0.001 TYR C 213 ARG 0.002 0.000 ARG D 172 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 554) hydrogen bonds : angle 4.24341 ( 1590) covalent geometry : bond 0.00325 (10672) covalent geometry : angle 0.50785 (14464) *********************** 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 147 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 1.467 Fit side-chains REVERT: A 107 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8295 (ttmm) REVERT: A 193 ASP cc_start: 0.8059 (m-30) cc_final: 0.7774 (m-30) REVERT: A 295 TRP cc_start: 0.8925 (OUTLIER) cc_final: 0.7315 (m-90) REVERT: B 295 TRP cc_start: 0.8918 (OUTLIER) cc_final: 0.7285 (m-90) REVERT: B 325 GLU cc_start: 0.7276 (tp30) cc_final: 0.6986 (mm-30) REVERT: C 295 TRP cc_start: 0.8904 (OUTLIER) cc_final: 0.7268 (m-90) REVERT: C 325 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6789 (mm-30) REVERT: D 86 LYS cc_start: 0.7791 (mtpt) cc_final: 0.7155 (mttp) outliers start: 40 outliers final: 32 residues processed: 137 average time/residue: 1.5457 time to fit residues: 227.8311 Evaluate side-chains 131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 295 TRP 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 295 TRP 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 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 TRP 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 212 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.137550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111795 restraints weight = 10860.560| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.45 r_work: 0.3139 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10672 Z= 0.168 Angle : 0.533 6.965 14464 Z= 0.268 Chirality : 0.041 0.138 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.204 56.303 1484 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.87 % Allowed : 14.21 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.23), residues: 1364 helix: 2.20 (0.19), residues: 720 sheet: -1.97 (0.30), residues: 216 loop : 0.38 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 295 HIS 0.004 0.001 HIS A 80 PHE 0.015 0.002 PHE C 144 TYR 0.016 0.002 TYR C 213 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 554) hydrogen bonds : angle 4.31067 ( 1590) covalent geometry : bond 0.00403 (10672) covalent geometry : angle 0.53281 (14464) *********************** 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: 43 poor density : 98 time to evaluate : 1.351 Fit side-chains REVERT: A 107 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8391 (ttmm) REVERT: A 295 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.7142 (m-90) REVERT: A 321 LYS cc_start: 0.6841 (mmtm) cc_final: 0.5789 (tptt) REVERT: B 295 TRP cc_start: 0.9049 (OUTLIER) cc_final: 0.7110 (m-90) REVERT: B 325 GLU cc_start: 0.7352 (tp30) cc_final: 0.7090 (mm-30) REVERT: C 247 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: C 295 TRP cc_start: 0.9039 (OUTLIER) cc_final: 0.7105 (m-90) REVERT: C 325 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: D 86 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7271 (mttp) outliers start: 43 outliers final: 32 residues processed: 132 average time/residue: 1.9463 time to fit residues: 276.3226 Evaluate side-chains 131 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 93 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 295 TRP 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 199 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 295 TRP 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 212 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 295 TRP 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 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 125 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3574 r_free = 0.3574 target = 0.140430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115623 restraints weight = 10861.873| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.37 r_work: 0.3181 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1462 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= 0.135 Angle : 0.507 6.780 14464 Z= 0.254 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.042 59.303 1482 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.87 % Allowed : 14.39 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.23), residues: 1364 helix: 2.29 (0.19), residues: 720 sheet: -1.99 (0.30), residues: 216 loop : 0.40 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 295 HIS 0.002 0.001 HIS D 80 PHE 0.013 0.001 PHE C 144 TYR 0.014 0.001 TYR C 213 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 554) hydrogen bonds : angle 4.21953 ( 1590) covalent geometry : bond 0.00320 (10672) covalent geometry : angle 0.50692 (14464) *********************** 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 145 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.218 Fit side-chains REVERT: A 107 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8320 (ttmm) REVERT: A 193 ASP cc_start: 0.8083 (m-30) cc_final: 0.7787 (m-30) REVERT: A 295 TRP cc_start: 0.9036 (OUTLIER) cc_final: 0.7104 (m-90) REVERT: A 321 LYS cc_start: 0.6848 (mmtm) cc_final: 0.5806 (tptt) REVERT: B 295 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.7067 (m-90) REVERT: B 325 GLU cc_start: 0.7342 (tp30) cc_final: 0.7126 (mm-30) REVERT: C 295 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.7085 (m-90) REVERT: C 325 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: D 86 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7347 (mttp) REVERT: D 193 ASP cc_start: 0.8088 (m-30) cc_final: 0.7822 (m-30) outliers start: 43 outliers final: 33 residues processed: 135 average time/residue: 1.3047 time to fit residues: 190.0023 Evaluate side-chains 130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 92 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 295 TRP 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 173 TYR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 295 TRP 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 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 TRP 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 182 ILE 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 83 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.140255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115385 restraints weight = 10740.285| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.36 r_work: 0.3179 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10672 Z= 0.140 Angle : 0.509 6.813 14464 Z= 0.255 Chirality : 0.040 0.134 1644 Planarity : 0.004 0.030 1880 Dihedral : 4.986 57.911 1482 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.14 % Allowed : 14.48 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1364 helix: 2.31 (0.19), residues: 720 sheet: -1.97 (0.30), residues: 216 loop : 0.39 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 295 HIS 0.002 0.001 HIS A 80 PHE 0.013 0.001 PHE C 144 TYR 0.015 0.001 TYR C 213 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 554) hydrogen bonds : angle 4.20310 ( 1590) covalent geometry : bond 0.00333 (10672) covalent geometry : angle 0.50886 (14464) *********************** 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 149 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 1.349 Fit side-chains REVERT: A 107 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8320 (ttmm) REVERT: A 193 ASP cc_start: 0.8112 (m-30) cc_final: 0.7817 (m-30) REVERT: A 295 TRP cc_start: 0.9064 (OUTLIER) cc_final: 0.7140 (m-90) REVERT: A 321 LYS cc_start: 0.6862 (mmtm) cc_final: 0.5820 (tptt) REVERT: B 193 ASP cc_start: 0.8110 (m-30) cc_final: 0.7766 (m-30) REVERT: B 295 TRP cc_start: 0.9056 (OUTLIER) cc_final: 0.7131 (m-90) REVERT: B 325 GLU cc_start: 0.7373 (tp30) cc_final: 0.7161 (mm-30) REVERT: C 193 ASP cc_start: 0.8128 (m-30) cc_final: 0.7795 (m-30) REVERT: C 295 TRP cc_start: 0.9053 (OUTLIER) cc_final: 0.7164 (m-90) REVERT: C 325 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6837 (mm-30) REVERT: D 86 LYS cc_start: 0.7991 (mtpt) cc_final: 0.7367 (mttp) REVERT: D 193 ASP cc_start: 0.8111 (m-30) cc_final: 0.7814 (m-30) outliers start: 46 outliers final: 36 residues processed: 137 average time/residue: 1.3298 time to fit residues: 196.8225 Evaluate side-chains 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 295 TRP 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 199 LYS Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 295 TRP 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 212 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 295 TRP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 92 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 82 optimal weight: 0.0370 chunk 83 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.144903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120164 restraints weight = 10747.536| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.37 r_work: 0.3261 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.110 Angle : 0.487 6.741 14464 Z= 0.243 Chirality : 0.039 0.129 1644 Planarity : 0.004 0.030 1880 Dihedral : 4.871 58.035 1482 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.69 % Allowed : 15.02 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1364 helix: 2.42 (0.19), residues: 720 sheet: -1.93 (0.31), residues: 216 loop : 0.45 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 295 HIS 0.001 0.000 HIS D 80 PHE 0.013 0.001 PHE D 144 TYR 0.013 0.001 TYR C 213 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 554) hydrogen bonds : angle 4.09596 ( 1590) covalent geometry : bond 0.00258 (10672) covalent geometry : angle 0.48721 (14464) *********************** 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 150 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.307 Fit side-chains REVERT: A 107 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8219 (ttmm) REVERT: A 193 ASP cc_start: 0.8051 (m-30) cc_final: 0.7693 (m-30) REVERT: A 295 TRP cc_start: 0.8997 (OUTLIER) cc_final: 0.7043 (m-90) REVERT: A 321 LYS cc_start: 0.6778 (mmtm) cc_final: 0.5725 (tptt) REVERT: B 86 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7091 (mtmt) REVERT: B 100 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7418 (tttp) REVERT: B 295 TRP cc_start: 0.9013 (OUTLIER) cc_final: 0.7007 (m-90) REVERT: B 325 GLU cc_start: 0.7310 (tp30) cc_final: 0.7081 (mm-30) REVERT: C 86 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7094 (mtmt) REVERT: C 164 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8343 (tmm) REVERT: C 193 ASP cc_start: 0.8141 (m-30) cc_final: 0.7746 (m-30) REVERT: C 295 TRP cc_start: 0.8992 (OUTLIER) cc_final: 0.7049 (m-90) REVERT: C 325 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6730 (mm-30) REVERT: D 86 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7320 (mttp) REVERT: D 100 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7283 (tttp) REVERT: D 164 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8436 (tmm) REVERT: D 193 ASP cc_start: 0.8072 (m-30) cc_final: 0.7751 (m-30) outliers start: 41 outliers final: 25 residues processed: 138 average time/residue: 1.4971 time to fit residues: 224.1458 Evaluate side-chains 138 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 295 TRP 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 173 TYR Chi-restraints excluded: chain B residue 295 TRP 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 295 TRP 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 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 96 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 125 optimal weight: 0.0670 chunk 9 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 168 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123004 restraints weight = 10643.060| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.26 r_work: 0.3251 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10672 Z= 0.117 Angle : 0.489 6.804 14464 Z= 0.245 Chirality : 0.040 0.132 1644 Planarity : 0.004 0.030 1880 Dihedral : 4.759 50.460 1482 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.33 % Allowed : 15.38 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1364 helix: 2.44 (0.19), residues: 720 sheet: -1.87 (0.31), residues: 216 loop : 0.47 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 295 HIS 0.002 0.000 HIS A 80 PHE 0.013 0.001 PHE D 144 TYR 0.012 0.001 TYR C 213 ARG 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03169 ( 554) hydrogen bonds : angle 4.10261 ( 1590) covalent geometry : bond 0.00275 (10672) covalent geometry : angle 0.48884 (14464) ********************** 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 140 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 1.159 Fit side-chains REVERT: A 107 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8179 (ttmm) REVERT: A 193 ASP cc_start: 0.8036 (m-30) cc_final: 0.7690 (m-30) REVERT: A 295 TRP cc_start: 0.8982 (OUTLIER) cc_final: 0.6997 (m-90) REVERT: A 321 LYS cc_start: 0.6727 (mmtm) cc_final: 0.5685 (tptt) REVERT: B 86 LYS cc_start: 0.7715 (mtpt) cc_final: 0.7016 (mtmt) REVERT: B 100 LYS cc_start: 0.7971 (mtpp) cc_final: 0.7382 (tttp) REVERT: B 193 ASP cc_start: 0.8101 (m-30) cc_final: 0.7720 (m-30) REVERT: B 295 TRP cc_start: 0.8970 (OUTLIER) cc_final: 0.6980 (m-90) REVERT: B 325 GLU cc_start: 0.7224 (tp30) cc_final: 0.6995 (mm-30) REVERT: C 86 LYS cc_start: 0.7727 (mtpt) cc_final: 0.7039 (mtmt) REVERT: C 295 TRP cc_start: 0.8942 (OUTLIER) cc_final: 0.6922 (m-90) REVERT: C 325 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: D 100 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7210 (tttp) REVERT: D 164 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8354 (tmm) REVERT: D 193 ASP cc_start: 0.8048 (m-30) cc_final: 0.7730 (m-30) outliers start: 37 outliers final: 27 residues processed: 128 average time/residue: 1.2114 time to fit residues: 168.4522 Evaluate side-chains 135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 173 TYR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 295 TRP 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 173 TYR Chi-restraints excluded: chain B residue 295 TRP 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 295 TRP Chi-restraints excluded: chain C residue 308 SER 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 182 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.141608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116236 restraints weight = 10709.069| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.39 r_work: 0.3228 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.133 Angle : 0.500 6.760 14464 Z= 0.251 Chirality : 0.040 0.134 1644 Planarity : 0.004 0.030 1880 Dihedral : 4.805 51.866 1482 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.06 % Allowed : 15.56 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1364 helix: 2.41 (0.19), residues: 720 sheet: -1.88 (0.31), residues: 216 loop : 0.46 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 295 HIS 0.002 0.001 HIS A 80 PHE 0.013 0.001 PHE D 144 TYR 0.013 0.001 TYR C 213 ARG 0.002 0.000 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 554) hydrogen bonds : angle 4.14808 ( 1590) covalent geometry : bond 0.00318 (10672) covalent geometry : angle 0.49978 (14464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7789.91 seconds wall clock time: 140 minutes 15.97 seconds (8415.97 seconds total)