Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 13:44:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2023/5k0z_8191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2023/5k0z_8191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2023/5k0z_8191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2023/5k0z_8191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2023/5k0z_8191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2023/5k0z_8191.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 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 52 5.16 5 C 6196 2.51 5 N 1636 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 268": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9749 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2427 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 307} Chain breaks: 2 Chain: "B" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2427 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 307} Chain breaks: 2 Chain: "C" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2427 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 307} Chain breaks: 2 Chain: "D" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2427 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 307} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Time building chain proxies: 5.67, per 1000 atoms: 0.58 Number of scatterers: 9749 At special positions: 0 Unit cell: (73.755, 97.515, 83.655, 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 52 16.00 O 1865 8.00 N 1636 7.00 C 6196 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 - 3.50 Amino acid : False - 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: 4.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 46.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 30 through 41 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.673A pdb=" N LYS A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.501A pdb=" N ASN A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Proline residue: A 121 - end of helix removed outlier: 3.595A pdb=" N TYR A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 162 through 176 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.999A pdb=" N HIS A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.673A pdb=" N LYS B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 109 through 127 removed outlier: 3.501A pdb=" N ASN B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) Proline residue: B 121 - end of helix removed outlier: 3.595A pdb=" N TYR B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 226 through 245 removed outlier: 4.000A pdb=" N HIS B 230 " --> pdb=" O TRP B 226 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 237 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.672A pdb=" N LYS C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 109 through 127 removed outlier: 3.501A pdb=" N ASN C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) Proline residue: C 121 - end of helix removed outlier: 3.595A pdb=" N TYR C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 162 through 176 Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 226 through 245 removed outlier: 4.000A pdb=" N HIS C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 237 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N TYR C 238 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 264 Processing helix chain 'C' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 54 through 66 removed outlier: 3.673A pdb=" N LYS D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 109 through 127 removed outlier: 3.502A pdb=" N ASN D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) Proline residue: D 121 - end of helix removed outlier: 3.595A pdb=" N TYR D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 162 through 176 Processing helix chain 'D' and resid 210 through 214 Processing helix chain 'D' and resid 226 through 245 removed outlier: 3.999A pdb=" N HIS D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 264 Processing helix chain 'D' and resid 308 through 327 removed outlier: 3.760A pdb=" N ILE D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.580A pdb=" N VAL C 293 " --> pdb=" O THR C 300 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL C 302 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 5.923A pdb=" N LEU A 47 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE A 132 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS A 185 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER A 201 " --> pdb=" O HIS A 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP A 187 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 275 removed outlier: 4.830A pdb=" N VAL A 302 " --> pdb=" O PRO A 291 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 293 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.579A pdb=" N VAL D 293 " --> pdb=" O THR D 300 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL D 302 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 75 through 78 removed outlier: 5.923A pdb=" N LEU B 47 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE B 132 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS B 185 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER B 201 " --> pdb=" O HIS B 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP B 187 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 275 removed outlier: 4.830A pdb=" N VAL B 302 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 293 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 75 through 78 removed outlier: 5.924A pdb=" N LEU C 47 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE C 132 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS C 185 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER C 201 " --> pdb=" O HIS C 185 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP C 187 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 75 through 78 removed outlier: 5.923A pdb=" N LEU D 47 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE D 132 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 184 through 190 removed outlier: 10.027A pdb=" N HIS D 185 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER D 201 " --> pdb=" O HIS D 185 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP D 187 " --> pdb=" O VAL D 199 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2690 1.33 - 1.45: 1393 1.45 - 1.57: 5705 1.57 - 1.68: 0 1.68 - 1.80: 76 Bond restraints: 9864 Sorted by residual: bond pdb=" CB CYS B 184 " pdb=" SG CYS B 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" CB CYS A 184 " pdb=" SG CYS A 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.62e+00 bond pdb=" CB CYS C 184 " pdb=" SG CYS C 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" CG LEU D 263 " pdb=" CD1 LEU D 263 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 ... (remaining 9859 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.60: 244 106.60 - 113.46: 5905 113.46 - 120.32: 3277 120.32 - 127.19: 3854 127.19 - 134.05: 104 Bond angle restraints: 13384 Sorted by residual: angle pdb=" C TYR D 126 " pdb=" N SER D 127 " pdb=" CA SER D 127 " ideal model delta sigma weight residual 122.74 119.03 3.71 1.06e+00 8.90e-01 1.23e+01 angle pdb=" C TYR B 126 " pdb=" N SER B 127 " pdb=" CA SER B 127 " ideal model delta sigma weight residual 122.74 119.05 3.69 1.06e+00 8.90e-01 1.21e+01 angle pdb=" C TYR A 126 " pdb=" N SER A 127 " pdb=" CA SER A 127 " ideal model delta sigma weight residual 122.74 119.07 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C TYR C 126 " pdb=" N SER C 127 " pdb=" CA SER C 127 " ideal model delta sigma weight residual 122.74 119.08 3.66 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CA GLN B 326 " pdb=" CB GLN B 326 " pdb=" CG GLN B 326 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 ... (remaining 13379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5704 17.61 - 35.22: 180 35.22 - 52.84: 20 52.84 - 70.45: 8 70.45 - 88.06: 12 Dihedral angle restraints: 5924 sinusoidal: 2284 harmonic: 3640 Sorted by residual: dihedral pdb=" CA GLY D 298 " pdb=" C GLY D 298 " pdb=" N LEU D 299 " pdb=" CA LEU D 299 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY A 298 " pdb=" C GLY A 298 " pdb=" N LEU A 299 " pdb=" CA LEU A 299 " ideal model delta harmonic sigma weight residual 180.00 158.62 21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY C 298 " pdb=" C GLY C 298 " pdb=" N LEU C 299 " pdb=" CA LEU C 299 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 5921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 924 0.044 - 0.087: 505 0.087 - 0.131: 146 0.131 - 0.175: 39 0.175 - 0.218: 18 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CA ASN D 225 " pdb=" N ASN D 225 " pdb=" C ASN D 225 " pdb=" CB ASN D 225 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN C 225 " pdb=" N ASN C 225 " pdb=" C ASN C 225 " pdb=" CB ASN C 225 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ASN A 225 " pdb=" N ASN A 225 " pdb=" C ASN A 225 " pdb=" CB ASN A 225 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1629 not shown) Planarity restraints: 1652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 118 " 0.023 2.00e-02 2.50e+03 1.81e-02 5.75e+00 pdb=" CG PHE D 118 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE D 118 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 118 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 118 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 118 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 118 " 0.023 2.00e-02 2.50e+03 1.80e-02 5.67e+00 pdb=" CG PHE C 118 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 118 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 118 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 118 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 118 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 118 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 118 " -0.023 2.00e-02 2.50e+03 1.80e-02 5.66e+00 pdb=" CG PHE A 118 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE A 118 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 118 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 118 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 118 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 118 " -0.006 2.00e-02 2.50e+03 ... (remaining 1649 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 143 2.62 - 3.19: 9617 3.19 - 3.76: 15515 3.76 - 4.33: 23988 4.33 - 4.90: 37950 Nonbonded interactions: 87213 Sorted by model distance: nonbonded pdb=" O THR B 16 " pdb=" CG2 VAL B 17 " model vdw 2.056 3.460 nonbonded pdb=" O THR D 16 " pdb=" CG2 VAL D 17 " model vdw 2.056 3.460 nonbonded pdb=" O THR C 16 " pdb=" CG2 VAL C 17 " model vdw 2.056 3.460 nonbonded pdb=" O THR A 16 " pdb=" CG2 VAL A 17 " model vdw 2.056 3.460 nonbonded pdb=" NZ LYS B 21 " pdb=" O VAL B 84 " model vdw 2.089 2.520 ... (remaining 87208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.370 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: 2.250 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.130 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5940 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 : 0.011 0.063 9864 Z= 0.728 Angle : 1.038 9.456 13384 Z= 0.572 Chirality : 0.059 0.218 1632 Planarity : 0.006 0.052 1652 Dihedral : 10.637 88.059 3572 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -4.11 (0.17), residues: 1244 helix: -3.65 (0.13), residues: 536 sheet: -2.52 (0.31), residues: 164 loop : -1.53 (0.20), residues: 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 518 average time/residue: 0.9653 time to fit residues: 542.1599 Evaluate side-chains 320 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.6053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 5.9990 chunk 93 optimal weight: 0.0370 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 304 ASN B 163 ASN B 304 ASN C 163 ASN C 304 ASN D 304 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9864 Z= 0.284 Angle : 0.850 9.198 13384 Z= 0.440 Chirality : 0.049 0.204 1632 Planarity : 0.006 0.036 1652 Dihedral : 5.405 15.408 1316 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 29.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 4.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.79 (0.21), residues: 1244 helix: -1.31 (0.19), residues: 536 sheet: -1.76 (0.33), residues: 168 loop : -0.60 (0.24), residues: 540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 416 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 13 residues processed: 432 average time/residue: 0.9483 time to fit residues: 445.0580 Evaluate side-chains 328 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 315 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.1845 time to fit residues: 2.7637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 chunk 76 optimal weight: 30.0000 chunk 31 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 9864 Z= 0.391 Angle : 0.831 7.219 13384 Z= 0.434 Chirality : 0.051 0.289 1632 Planarity : 0.005 0.041 1652 Dihedral : 5.254 14.541 1316 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 5.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.85 (0.22), residues: 1244 helix: -0.45 (0.21), residues: 540 sheet: -1.50 (0.34), residues: 168 loop : -0.10 (0.26), residues: 536 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 342 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 33 residues processed: 377 average time/residue: 1.0328 time to fit residues: 421.4877 Evaluate side-chains 308 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 275 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 26 residues processed: 7 average time/residue: 0.6115 time to fit residues: 6.4007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 50.0000 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 0.0670 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 overall best weight: 6.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 9864 Z= 0.289 Angle : 0.809 9.552 13384 Z= 0.410 Chirality : 0.047 0.213 1632 Planarity : 0.005 0.053 1652 Dihedral : 5.203 17.583 1316 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 27.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 7.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.39 (0.23), residues: 1244 helix: -0.05 (0.22), residues: 520 sheet: -1.45 (0.36), residues: 160 loop : 0.16 (0.27), residues: 564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 326 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 38 residues processed: 383 average time/residue: 0.9372 time to fit residues: 391.5391 Evaluate side-chains 320 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 282 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 27 residues processed: 11 average time/residue: 0.8649 time to fit residues: 11.9915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 80.0000 chunk 61 optimal weight: 30.0000 chunk 107 optimal weight: 0.0370 chunk 30 optimal weight: 6.9990 overall best weight: 4.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS B 20 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS C 155 HIS D 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 9864 Z= 0.275 Angle : 0.830 9.815 13384 Z= 0.416 Chirality : 0.048 0.277 1632 Planarity : 0.004 0.037 1652 Dihedral : 5.167 17.096 1316 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 26.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 5.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.04 (0.24), residues: 1244 helix: 0.24 (0.23), residues: 516 sheet: -1.32 (0.41), residues: 132 loop : 0.38 (0.27), residues: 596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 338 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 34 residues processed: 379 average time/residue: 0.9801 time to fit residues: 403.3159 Evaluate side-chains 309 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 275 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 7 average time/residue: 0.4232 time to fit residues: 5.1956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 40.0000 chunk 107 optimal weight: 40.0000 chunk 23 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 50.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 163 ASN ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 9864 Z= 0.337 Angle : 0.875 9.360 13384 Z= 0.442 Chirality : 0.049 0.264 1632 Planarity : 0.005 0.048 1652 Dihedral : 5.191 17.857 1316 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.17 (0.25), residues: 1244 helix: 0.33 (0.23), residues: 516 sheet: -1.28 (0.42), residues: 132 loop : 0.48 (0.28), residues: 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 310 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 39 residues processed: 353 average time/residue: 0.8171 time to fit residues: 318.1485 Evaluate side-chains 305 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 266 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 9 average time/residue: 0.6811 time to fit residues: 8.3353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 214 ASN A 232 GLN B 232 GLN C 20 ASN C 214 ASN D 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.7346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9864 Z= 0.304 Angle : 0.897 9.877 13384 Z= 0.449 Chirality : 0.051 0.270 1632 Planarity : 0.005 0.055 1652 Dihedral : 5.264 19.194 1316 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 30.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 5.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.30 (0.25), residues: 1244 helix: 0.42 (0.23), residues: 512 sheet: 0.13 (0.53), residues: 92 loop : 0.18 (0.27), residues: 640 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 38 residues processed: 360 average time/residue: 0.8609 time to fit residues: 342.3452 Evaluate side-chains 305 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 29 residues processed: 10 average time/residue: 0.5053 time to fit residues: 7.4409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 40.0000 chunk 59 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN A 232 GLN C 204 ASN D 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.7532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 9864 Z= 0.289 Angle : 0.926 11.133 13384 Z= 0.457 Chirality : 0.052 0.318 1632 Planarity : 0.005 0.050 1652 Dihedral : 5.309 19.089 1316 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 30.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 5.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.36 (0.25), residues: 1244 helix: 0.43 (0.23), residues: 508 sheet: -0.03 (0.54), residues: 92 loop : 0.29 (0.27), residues: 644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 338 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 35 residues processed: 377 average time/residue: 0.8208 time to fit residues: 340.7848 Evaluate side-chains 324 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 24 residues processed: 11 average time/residue: 0.5242 time to fit residues: 8.2375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN B 20 ASN ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 9864 Z= 0.336 Angle : 1.021 13.083 13384 Z= 0.503 Chirality : 0.056 0.359 1632 Planarity : 0.005 0.052 1652 Dihedral : 5.461 20.994 1316 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 32.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.07 (0.25), residues: 1244 helix: 0.12 (0.23), residues: 512 sheet: -0.08 (0.54), residues: 92 loop : 0.19 (0.27), residues: 640 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 324 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 357 average time/residue: 0.8907 time to fit residues: 348.5007 Evaluate side-chains 320 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 12 average time/residue: 0.3985 time to fit residues: 7.3677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN C 326 GLN D 163 ASN D 204 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.7799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 9864 Z= 0.349 Angle : 1.082 13.661 13384 Z= 0.534 Chirality : 0.057 0.360 1632 Planarity : 0.005 0.053 1652 Dihedral : 5.575 18.322 1316 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 33.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 4.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.39 (0.24), residues: 1244 helix: -0.14 (0.23), residues: 512 sheet: -1.15 (0.45), residues: 124 loop : 0.04 (0.26), residues: 608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 296 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 30 residues processed: 325 average time/residue: 0.8132 time to fit residues: 292.2157 Evaluate side-chains 308 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 278 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 21 residues processed: 9 average time/residue: 0.6145 time to fit residues: 7.8507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 98 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 18 optimal weight: 0.0870 chunk 86 optimal weight: 9.9990 overall best weight: 7.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 326 GLN ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 326 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.079232 restraints weight = 27340.427| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 5.20 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.7964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 9864 Z= 0.348 Angle : 1.089 13.201 13384 Z= 0.538 Chirality : 0.057 0.356 1632 Planarity : 0.006 0.068 1652 Dihedral : 5.628 18.628 1316 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 33.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 4.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.35 (0.24), residues: 1244 helix: -0.32 (0.23), residues: 512 sheet: -0.17 (0.54), residues: 92 loop : 0.01 (0.26), residues: 640 =============================================================================== Job complete usr+sys time: 5239.99 seconds wall clock time: 93 minutes 29.87 seconds (5609.87 seconds total)