Starting phenix.real_space_refine on Tue May 13 15:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8twl_41670/05_2025/8twl_41670.cif Found real_map, /net/cci-nas-00/data/ceres_data/8twl_41670/05_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_41670/05_2025/8twl_41670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8twl_41670/05_2025/8twl_41670.map" model { file = "/net/cci-nas-00/data/ceres_data/8twl_41670/05_2025/8twl_41670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8twl_41670/05_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-5687/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: 6.48, per 1000 atoms: 0.60 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: 2.44 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: 1.30 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: 3.31 Time building geometry restraints manager: 2.87 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: 0.960 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.200 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.260 ------------------------------------------------------------------------------- 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 : 1.130 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: 1.3650 time to fit residues: 183.2109 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 : 1.181 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118714 restraints weight = 10616.838| |-----------------------------------------------------------------------------| 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: 2.99 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 1.215 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 124 average time/residue: 1.5975 time to fit residues: 210.9090 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 : 1.183 ------------------------------------------------------------------------------- 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: 3.9990 chunk 110 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 136 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.112413 restraints weight = 10756.591| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.36 r_work: 0.3127 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1171 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= 0.214 Angle : 0.579 7.257 14464 Z= 0.293 Chirality : 0.043 0.145 1644 Planarity : 0.004 0.031 1880 Dihedral : 5.468 52.763 1488 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.87 % Allowed : 13.76 % 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: -1.93 (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 0.018 0.002 TYR C 213 ARG 0.003 0.001 ARG D 258 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 554) hydrogen bonds : angle 4.50121 ( 1590) covalent geometry : bond 0.00515 (10672) covalent geometry : angle 0.57870 (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 154 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.253 Fit side-chains REVERT: A 107 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8402 (ttmm) REVERT: A 321 LYS cc_start: 0.6741 (mmtm) cc_final: 0.5735 (tptt) REVERT: B 152 LYS cc_start: 0.8221 (pttp) cc_final: 0.8007 (pttp) REVERT: B 325 GLU cc_start: 0.7352 (tp30) cc_final: 0.7139 (mm-30) REVERT: C 247 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: C 321 LYS cc_start: 0.7535 (tttm) cc_final: 0.7293 (tptt) REVERT: D 86 LYS cc_start: 0.7897 (mtpt) cc_final: 0.7324 (mttp) REVERT: D 321 LYS cc_start: 0.6791 (mmtm) cc_final: 0.5759 (tptt) outliers start: 43 outliers final: 32 residues processed: 142 average time/residue: 1.4097 time to fit residues: 214.5217 Evaluate side-chains 129 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain 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: 5.9990 chunk 133 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 64 optimal weight: 0.0170 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 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 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 = 0.3569 r_free = 0.3569 target = 0.140116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114858 restraints weight = 10663.627| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.37 r_work: 0.3217 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1272 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= 0.139 Angle : 0.514 7.061 14464 Z= 0.258 Chirality : 0.040 0.135 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.327 56.509 1488 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.87 % Allowed : 13.94 % 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: 1.37 (0.23), residues: 1364 helix: 2.22 (0.19), residues: 720 sheet: -2.02 (0.30), residues: 216 loop : 0.42 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 147 HIS 0.002 0.000 HIS D 80 PHE 0.013 0.002 PHE C 144 TYR 0.014 0.001 TYR B 213 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 554) hydrogen bonds : angle 4.32162 ( 1590) covalent geometry : bond 0.00328 (10672) covalent geometry : angle 0.51392 (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 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 1.233 Fit side-chains REVERT: A 107 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8348 (ttmm) REVERT: A 247 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: A 295 TRP cc_start: 0.8924 (OUTLIER) cc_final: 0.7271 (m-90) REVERT: B 295 TRP cc_start: 0.8909 (OUTLIER) cc_final: 0.7227 (m-90) REVERT: B 325 GLU cc_start: 0.7296 (tp30) cc_final: 0.7046 (mm-30) REVERT: C 295 TRP cc_start: 0.8882 (OUTLIER) cc_final: 0.7303 (m-90) REVERT: C 325 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7220 (mm-30) REVERT: D 86 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7307 (mttp) outliers start: 43 outliers final: 33 residues processed: 124 average time/residue: 1.3513 time to fit residues: 180.4828 Evaluate side-chains 121 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 247 GLU 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: 0.2980 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 15 optimal weight: 0.0170 chunk 83 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.141721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116520 restraints weight = 10640.356| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.38 r_work: 0.3223 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.122 Angle : 0.498 6.932 14464 Z= 0.247 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.030 1880 Dihedral : 5.251 58.613 1488 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.23 % Allowed : 14.03 % 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: 1.48 (0.23), residues: 1364 helix: 2.33 (0.19), residues: 720 sheet: -2.00 (0.31), residues: 216 loop : 0.44 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 295 HIS 0.002 0.000 HIS A 80 PHE 0.012 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 0.03312 ( 554) hydrogen bonds : angle 4.18225 ( 1590) covalent geometry : bond 0.00288 (10672) covalent geometry : angle 0.49752 (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 157 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 1.316 Fit side-chains REVERT: A 107 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8300 (ttmm) REVERT: A 193 ASP cc_start: 0.8101 (m-30) cc_final: 0.7781 (m-30) REVERT: A 295 TRP cc_start: 0.8967 (OUTLIER) cc_final: 0.7308 (m-90) REVERT: B 295 TRP cc_start: 0.8951 (OUTLIER) cc_final: 0.7284 (m-90) REVERT: B 325 GLU cc_start: 0.7330 (tp30) cc_final: 0.7041 (mm-30) REVERT: C 164 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8447 (tmm) REVERT: C 295 TRP cc_start: 0.8943 (OUTLIER) cc_final: 0.7270 (m-90) REVERT: C 325 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6878 (mm-30) REVERT: D 86 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7261 (mttp) REVERT: D 193 ASP cc_start: 0.8109 (m-30) cc_final: 0.7798 (m-30) outliers start: 47 outliers final: 32 residues processed: 143 average time/residue: 1.2952 time to fit residues: 199.7144 Evaluate side-chains 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 95 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 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 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 270 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 341 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 0.0470 chunk 31 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.4136 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.147901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125417 restraints weight = 10659.263| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.25 r_work: 0.3282 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1523 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= 0.109 Angle : 0.482 6.775 14464 Z= 0.240 Chirality : 0.039 0.127 1644 Planarity : 0.003 0.032 1880 Dihedral : 5.017 58.763 1484 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.96 % Allowed : 14.30 % 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: 1.61 (0.24), residues: 1364 helix: 2.44 (0.19), residues: 720 sheet: -1.94 (0.31), residues: 216 loop : 0.49 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 295 HIS 0.002 0.000 HIS A 80 PHE 0.012 0.001 PHE D 144 TYR 0.012 0.001 TYR C 213 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 554) hydrogen bonds : angle 4.07540 ( 1590) covalent geometry : bond 0.00255 (10672) covalent geometry : angle 0.48228 (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 153 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.339 Fit side-chains REVERT: A 107 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8169 (ttmm) REVERT: A 295 TRP cc_start: 0.8979 (OUTLIER) cc_final: 0.7152 (m-90) REVERT: B 164 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8238 (tmm) REVERT: B 295 TRP cc_start: 0.8978 (OUTLIER) cc_final: 0.7152 (m-90) REVERT: B 325 GLU cc_start: 0.7280 (tp30) cc_final: 0.6989 (mm-30) REVERT: C 295 TRP cc_start: 0.8962 (OUTLIER) cc_final: 0.7145 (m-90) REVERT: C 325 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7072 (mm-30) REVERT: D 86 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7275 (mttp) REVERT: D 164 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8398 (tmm) outliers start: 44 outliers final: 28 residues processed: 137 average time/residue: 1.2925 time to fit residues: 191.6189 Evaluate side-chains 133 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 295 TRP Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 341 LYS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 173 TYR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 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 Chi-restraints excluded: chain D residue 341 LYS 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: 1.9990 chunk 44 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.138644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113208 restraints weight = 10914.304| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.40 r_work: 0.3134 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10672 Z= 0.165 Angle : 0.526 6.935 14464 Z= 0.265 Chirality : 0.041 0.140 1644 Planarity : 0.004 0.032 1880 Dihedral : 5.061 55.306 1482 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.69 % Allowed : 14.66 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.23), residues: 1364 helix: 2.48 (0.19), residues: 696 sheet: -1.90 (0.30), residues: 216 loop : 0.35 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 295 HIS 0.003 0.001 HIS D 80 PHE 0.015 0.002 PHE B 144 TYR 0.016 0.002 TYR C 213 ARG 0.003 0.000 ARG B 258 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 554) hydrogen bonds : angle 4.24748 ( 1590) covalent geometry : bond 0.00395 (10672) covalent geometry : angle 0.52598 (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 135 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 94 time to evaluate : 1.214 Fit side-chains REVERT: A 107 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8350 (ttmm) REVERT: A 193 ASP cc_start: 0.8120 (m-30) cc_final: 0.7778 (m-30) REVERT: A 295 TRP cc_start: 0.9083 (OUTLIER) cc_final: 0.7157 (m-90) REVERT: A 321 LYS cc_start: 0.6726 (mmtm) cc_final: 0.5782 (tptt) REVERT: B 193 ASP cc_start: 0.8155 (m-30) cc_final: 0.7777 (m-30) REVERT: B 295 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.7136 (m-90) REVERT: B 325 GLU cc_start: 0.7327 (tp30) cc_final: 0.7070 (mm-30) REVERT: C 295 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.7192 (m-90) REVERT: C 325 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: D 86 LYS cc_start: 0.7901 (mtpt) cc_final: 0.7274 (mttp) REVERT: D 193 ASP cc_start: 0.8147 (m-30) cc_final: 0.7804 (m-30) outliers start: 41 outliers final: 32 residues processed: 127 average time/residue: 1.2434 time to fit residues: 170.6015 Evaluate side-chains 128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 172 ARG 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 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 320 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 212 VAL 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: 1.9990 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 30 optimal weight: 0.0570 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.143876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119991 restraints weight = 10640.094| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.27 r_work: 0.3219 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.131 Angle : 0.499 6.829 14464 Z= 0.250 Chirality : 0.040 0.132 1644 Planarity : 0.003 0.031 1880 Dihedral : 4.970 52.658 1482 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.42 % Allowed : 14.93 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.23), residues: 1364 helix: 2.37 (0.19), residues: 720 sheet: -1.94 (0.30), residues: 216 loop : 0.48 (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 0.014 0.001 TYR B 213 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 554) hydrogen bonds : angle 4.18598 ( 1590) covalent geometry : bond 0.00310 (10672) covalent geometry : angle 0.49891 (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 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 1.118 Fit side-chains REVERT: A 107 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8272 (ttmm) REVERT: A 193 ASP cc_start: 0.8072 (m-30) cc_final: 0.7743 (m-30) REVERT: A 295 TRP cc_start: 0.9000 (OUTLIER) cc_final: 0.6988 (m-90) REVERT: A 321 LYS cc_start: 0.6831 (mmtm) cc_final: 0.5779 (tptt) REVERT: B 295 TRP cc_start: 0.9027 (OUTLIER) cc_final: 0.6964 (m-90) REVERT: B 325 GLU cc_start: 0.7267 (tp30) cc_final: 0.7046 (mm-30) REVERT: C 193 ASP cc_start: 0.8087 (m-30) cc_final: 0.7715 (m-30) REVERT: C 295 TRP cc_start: 0.8989 (OUTLIER) cc_final: 0.6994 (m-90) REVERT: C 325 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: D 86 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7290 (mttp) REVERT: D 193 ASP cc_start: 0.8090 (m-30) cc_final: 0.7773 (m-30) outliers start: 38 outliers final: 31 residues processed: 131 average time/residue: 1.2027 time to fit residues: 170.7614 Evaluate side-chains 136 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 182 ILE 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 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: 0.9980 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN B 241 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 GLN D 241 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119538 restraints weight = 10769.355| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.27 r_work: 0.3240 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1543 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= 0.134 Angle : 0.502 6.836 14464 Z= 0.252 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.031 1880 Dihedral : 4.944 52.821 1482 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.69 % Allowed : 14.66 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.23), residues: 1364 helix: 2.37 (0.19), residues: 720 sheet: -1.93 (0.31), residues: 216 loop : 0.47 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.002 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 554) hydrogen bonds : angle 4.17410 ( 1590) covalent geometry : bond 0.00320 (10672) covalent geometry : angle 0.50206 (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 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 1.132 Fit side-chains REVERT: A 107 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8289 (ttmm) REVERT: A 193 ASP cc_start: 0.8102 (m-30) cc_final: 0.7746 (m-30) REVERT: A 295 TRP cc_start: 0.9022 (OUTLIER) cc_final: 0.7064 (m-90) REVERT: A 321 LYS cc_start: 0.6846 (mmtm) cc_final: 0.5821 (tptt) REVERT: B 295 TRP cc_start: 0.9037 (OUTLIER) cc_final: 0.7075 (m-90) REVERT: B 325 GLU cc_start: 0.7318 (tp30) cc_final: 0.7101 (mm-30) REVERT: C 193 ASP cc_start: 0.8141 (m-30) cc_final: 0.7771 (m-30) REVERT: C 295 TRP cc_start: 0.9011 (OUTLIER) cc_final: 0.7093 (m-90) REVERT: C 325 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: D 86 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7357 (mttp) REVERT: D 100 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7282 (tttp) REVERT: D 193 ASP cc_start: 0.8133 (m-30) cc_final: 0.7792 (m-30) outliers start: 41 outliers final: 35 residues processed: 129 average time/residue: 1.2185 time to fit residues: 170.8490 Evaluate side-chains 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 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 182 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.140752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115778 restraints weight = 10793.237| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.37 r_work: 0.3225 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1556 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= 0.143 Angle : 0.508 6.788 14464 Z= 0.255 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.030 1880 Dihedral : 4.940 54.936 1482 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.87 % Allowed : 14.48 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.52 (0.23), residues: 1364 helix: 2.35 (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 0.015 0.002 TRP C 295 HIS 0.003 0.001 HIS D 80 PHE 0.014 0.002 PHE C 144 TYR 0.015 0.001 TYR C 213 ARG 0.002 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 554) hydrogen bonds : angle 4.20236 ( 1590) covalent geometry : bond 0.00342 (10672) covalent geometry : angle 0.50842 (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 139 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 1.497 Fit side-chains REVERT: A 107 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8307 (ttmm) REVERT: A 193 ASP cc_start: 0.8110 (m-30) cc_final: 0.7753 (m-30) REVERT: A 295 TRP cc_start: 0.9030 (OUTLIER) cc_final: 0.7082 (m-90) REVERT: A 321 LYS cc_start: 0.6847 (mmtm) cc_final: 0.5805 (tptt) REVERT: B 295 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.7002 (m-90) REVERT: B 325 GLU cc_start: 0.7346 (tp30) cc_final: 0.7127 (mm-30) REVERT: C 193 ASP cc_start: 0.8124 (m-30) cc_final: 0.7742 (m-30) REVERT: C 295 TRP cc_start: 0.9034 (OUTLIER) cc_final: 0.7020 (m-90) REVERT: C 325 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6841 (mm-30) REVERT: D 86 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7344 (mttp) REVERT: D 100 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7234 (tttp) REVERT: D 193 ASP cc_start: 0.8131 (m-30) cc_final: 0.7780 (m-30) outliers start: 43 outliers final: 35 residues processed: 129 average time/residue: 1.2200 time to fit residues: 170.8406 Evaluate side-chains 137 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 172 ARG 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 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 182 ILE Chi-restraints excluded: chain C residue 212 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 31 optimal weight: 0.0020 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 83 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 overall best weight: 0.3466 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.146727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122203 restraints weight = 10671.901| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.36 r_work: 0.3297 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10672 Z= 0.102 Angle : 0.479 6.744 14464 Z= 0.239 Chirality : 0.039 0.125 1644 Planarity : 0.003 0.030 1880 Dihedral : 4.731 54.678 1482 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.33 % Allowed : 15.20 % Favored : 81.47 % 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: 1.65 (0.24), residues: 1364 helix: 2.47 (0.19), residues: 720 sheet: -1.93 (0.31), residues: 216 loop : 0.51 (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 A 80 PHE 0.012 0.001 PHE D 144 TYR 0.012 0.001 TYR C 213 ARG 0.003 0.000 ARG A 200 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 554) hydrogen bonds : angle 4.03794 ( 1590) covalent geometry : bond 0.00236 (10672) covalent geometry : angle 0.47939 (14464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7157.95 seconds wall clock time: 124 minutes 31.92 seconds (7471.92 seconds total)