Starting phenix.real_space_refine on Sun Apr 7 06:02:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2024/5k0z_8191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2024/5k0z_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_2024/5k0z_8191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2024/5k0z_8191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2024/5k0z_8191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k0z_8191/04_2024/5k0z_8191.pdb" } resolution = 2.8 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= 0.003 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-dev-5288/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: 5.38, per 1000 atoms: 0.55 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: 3.82 Conformation dependent library (CDL) restraints added in 1.8 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: 1.06 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: 3.04 Time building geometry restraints manager: 4.17 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: 2.010 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.010 Find NCS groups from input model: 0.620 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.290 ------------------------------------------------------------------------------- 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 % Allowed : 1.82 % Favored : 98.18 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.005 TRP C 147 HIS 0.010 0.003 HIS C 180 PHE 0.041 0.008 PHE D 118 TYR 0.022 0.003 TYR D 82 ARG 0.007 0.001 ARG B 242 *********************** 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 : 1.277 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: A 55 ASP cc_start: 0.5770 (p0) cc_final: 0.5431 (p0) REVERT: A 328 ASP cc_start: 0.6820 (p0) cc_final: 0.6499 (p0) REVERT: B 55 ASP cc_start: 0.5735 (p0) cc_final: 0.5448 (p0) REVERT: B 268 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6461 (mtm180) REVERT: B 328 ASP cc_start: 0.6840 (p0) cc_final: 0.6517 (p0) REVERT: C 55 ASP cc_start: 0.5777 (p0) cc_final: 0.5481 (p0) REVERT: C 328 ASP cc_start: 0.6801 (p0) cc_final: 0.6481 (p0) REVERT: D 55 ASP cc_start: 0.5785 (p0) cc_final: 0.5490 (p0) REVERT: D 328 ASP cc_start: 0.6820 (p0) cc_final: 0.6501 (p0) outliers start: 0 outliers final: 1 residues processed: 518 average time/residue: 0.9936 time to fit residues: 557.9955 Evaluate side-chains 324 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 323 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE 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: 0.6023 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9864 Z= 0.269 Angle : 0.842 9.365 13384 Z= 0.437 Chirality : 0.049 0.204 1632 Planarity : 0.006 0.037 1652 Dihedral : 5.437 25.821 1318 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 29.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.64 % Allowed : 21.27 % Favored : 74.09 % 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: -1.28 (0.19), residues: 536 sheet: -1.72 (0.33), residues: 168 loop : -0.66 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 200 HIS 0.004 0.001 HIS D 185 PHE 0.018 0.003 PHE B 70 TYR 0.026 0.003 TYR D 171 ARG 0.005 0.001 ARG B 156 *********************** 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 468 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 417 time to evaluate : 0.990 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: A 188 ILE cc_start: 0.6754 (mp) cc_final: 0.6490 (mp) REVERT: A 268 ARG cc_start: 0.6923 (mtm180) cc_final: 0.6651 (ttp80) REVERT: A 310 ASP cc_start: 0.6530 (OUTLIER) cc_final: 0.6295 (p0) REVERT: B 188 ILE cc_start: 0.6752 (mp) cc_final: 0.6501 (mp) REVERT: B 310 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.6313 (p0) REVERT: C 188 ILE cc_start: 0.6736 (mp) cc_final: 0.6490 (mp) REVERT: C 268 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6554 (ttp80) REVERT: C 310 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.6323 (p0) REVERT: D 188 ILE cc_start: 0.6741 (mp) cc_final: 0.6485 (mp) REVERT: D 268 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6464 (ttp80) REVERT: D 310 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.6322 (p0) outliers start: 51 outliers final: 13 residues processed: 433 average time/residue: 0.9884 time to fit residues: 464.9286 Evaluate side-chains 331 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 312 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 310 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 268 ARG Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 310 ASP Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 310 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 0.3980 chunk 76 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 overall best weight: 6.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 305 GLN C 305 GLN D 305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9864 Z= 0.307 Angle : 0.814 8.163 13384 Z= 0.417 Chirality : 0.051 0.322 1632 Planarity : 0.005 0.032 1652 Dihedral : 5.141 15.738 1316 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.73 % Allowed : 28.91 % Favored : 66.36 % 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: -0.87 (0.22), residues: 1244 helix: -0.36 (0.21), residues: 532 sheet: -1.62 (0.35), residues: 168 loop : -0.22 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 187 HIS 0.003 0.001 HIS D 180 PHE 0.018 0.003 PHE C 169 TYR 0.021 0.003 TYR B 171 ARG 0.004 0.001 ARG D 111 *********************** 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: 52 poor density : 355 time to evaluate : 1.105 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: A 46 GLU cc_start: 0.4759 (tp30) cc_final: 0.4420 (tp30) outliers start: 52 outliers final: 15 residues processed: 380 average time/residue: 1.0249 time to fit residues: 421.6764 Evaluate side-chains 298 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 283 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 173 MET Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 276 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 30.0000 chunk 84 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 40.0000 chunk 119 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 GLN ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.6179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9864 Z= 0.368 Angle : 0.830 9.445 13384 Z= 0.424 Chirality : 0.048 0.212 1632 Planarity : 0.005 0.051 1652 Dihedral : 5.251 18.530 1316 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.82 % Allowed : 30.64 % Favored : 62.55 % 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: -0.50 (0.23), residues: 1244 helix: 0.05 (0.23), residues: 508 sheet: -1.58 (0.36), residues: 160 loop : -0.10 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 249 HIS 0.005 0.001 HIS C 180 PHE 0.019 0.003 PHE B 70 TYR 0.028 0.003 TYR D 171 ARG 0.011 0.002 ARG B 268 *********************** 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 399 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 324 time to evaluate : 1.196 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: 75 outliers final: 29 residues processed: 376 average time/residue: 1.0226 time to fit residues: 416.7253 Evaluate side-chains 322 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 70.0000 chunk 61 optimal weight: 30.0000 chunk 107 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 HIS ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9864 Z= 0.348 Angle : 0.855 9.265 13384 Z= 0.432 Chirality : 0.049 0.271 1632 Planarity : 0.005 0.037 1652 Dihedral : 5.277 16.818 1316 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 28.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.00 % Allowed : 31.82 % Favored : 62.18 % 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: 0.06 (0.25), residues: 1244 helix: 0.32 (0.23), residues: 516 sheet: -1.19 (0.42), residues: 132 loop : 0.30 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 249 HIS 0.005 0.001 HIS C 180 PHE 0.020 0.004 PHE A 70 TYR 0.034 0.003 TYR C 171 ARG 0.011 0.002 ARG B 268 *********************** 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 393 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 327 time to evaluate : 1.134 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: C 217 MET cc_start: 0.6299 (ptm) cc_final: 0.6091 (ptm) outliers start: 66 outliers final: 34 residues processed: 369 average time/residue: 0.9507 time to fit residues: 382.2081 Evaluate side-chains 308 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 274 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 251 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 324 SER 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: 20.0000 chunk 23 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9864 Z= 0.290 Angle : 0.861 11.008 13384 Z= 0.434 Chirality : 0.050 0.222 1632 Planarity : 0.005 0.034 1652 Dihedral : 5.223 17.688 1316 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 28.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.91 % Allowed : 37.45 % Favored : 58.64 % 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: 0.16 (0.25), residues: 1244 helix: 0.42 (0.24), residues: 504 sheet: -1.14 (0.44), residues: 132 loop : 0.32 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 226 HIS 0.004 0.001 HIS D 180 PHE 0.025 0.004 PHE D 70 TYR 0.025 0.002 TYR D 171 ARG 0.012 0.002 ARG B 268 *********************** 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 377 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 334 time to evaluate : 1.174 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: 43 outliers final: 21 residues processed: 362 average time/residue: 0.9661 time to fit residues: 380.2746 Evaluate side-chains 309 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 288 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 276 VAL 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: 7.9990 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 40.0000 chunk 66 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 ASN B 204 ASN C 20 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9864 Z= 0.302 Angle : 0.898 10.490 13384 Z= 0.446 Chirality : 0.050 0.227 1632 Planarity : 0.005 0.048 1652 Dihedral : 5.248 19.940 1316 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.00 % Allowed : 38.27 % Favored : 56.73 % 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: 0.26 (0.25), residues: 1244 helix: 0.47 (0.24), residues: 508 sheet: 0.08 (0.55), residues: 92 loop : 0.09 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 226 HIS 0.006 0.001 HIS C 180 PHE 0.029 0.004 PHE D 70 TYR 0.025 0.002 TYR D 171 ARG 0.011 0.002 ARG B 168 *********************** 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 364 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 309 time to evaluate : 1.164 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: 55 outliers final: 32 residues processed: 344 average time/residue: 0.8667 time to fit residues: 328.6160 Evaluate side-chains 319 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 287 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6135 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9864 Z= 0.334 Angle : 0.952 11.515 13384 Z= 0.473 Chirality : 0.052 0.261 1632 Planarity : 0.005 0.053 1652 Dihedral : 5.315 21.258 1316 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 30.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.09 % Allowed : 38.82 % Favored : 56.09 % 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: 0.19 (0.25), residues: 1244 helix: 0.37 (0.23), residues: 508 sheet: 0.04 (0.57), residues: 92 loop : 0.09 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 226 HIS 0.006 0.001 HIS C 180 PHE 0.026 0.004 PHE C 70 TYR 0.020 0.002 TYR C 171 ARG 0.013 0.002 ARG B 268 *********************** 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 352 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 296 time to evaluate : 1.120 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 outliers start: 56 outliers final: 30 residues processed: 333 average time/residue: 0.7893 time to fit residues: 291.2638 Evaluate side-chains 314 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 284 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 19 SER Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 30.0000 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 326 GLN B 204 ASN C 214 ASN C 326 GLN D 326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9864 Z= 0.290 Angle : 0.991 12.285 13384 Z= 0.487 Chirality : 0.053 0.272 1632 Planarity : 0.005 0.050 1652 Dihedral : 5.367 20.194 1316 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.64 % Allowed : 40.27 % Favored : 56.09 % 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: 0.26 (0.24), residues: 496 sheet: 0.10 (0.59), residues: 92 loop : 0.01 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 226 HIS 0.005 0.001 HIS C 180 PHE 0.026 0.004 PHE B 70 TYR 0.024 0.002 TYR D 171 ARG 0.012 0.001 ARG B 268 *********************** 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 375 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 335 time to evaluate : 1.135 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: B 257 GLU cc_start: 0.4105 (tp30) cc_final: 0.3896 (tp30) outliers start: 40 outliers final: 28 residues processed: 357 average time/residue: 0.9119 time to fit residues: 356.4184 Evaluate side-chains 312 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 10.0000 chunk 71 optimal weight: 40.0000 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN D 20 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.7982 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= 0.338 Angle : 1.073 13.133 13384 Z= 0.532 Chirality : 0.055 0.285 1632 Planarity : 0.005 0.053 1652 Dihedral : 5.654 21.320 1316 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 33.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.82 % Allowed : 42.55 % Favored : 54.64 % 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: -0.26 (0.24), residues: 1244 helix: -0.15 (0.23), residues: 496 sheet: 0.05 (0.58), residues: 92 loop : -0.07 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 226 HIS 0.005 0.001 HIS C 180 PHE 0.031 0.005 PHE B 116 TYR 0.030 0.002 TYR B 246 ARG 0.011 0.001 ARG B 168 ********************** 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 334 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 303 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 25 residues processed: 317 average time/residue: 0.8747 time to fit residues: 304.2936 Evaluate side-chains 292 residues out of total 1100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 267 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 90 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 40.0000 chunk 86 optimal weight: 0.7980 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 232 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN B 204 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS D 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.105324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084717 restraints weight = 26825.801| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 5.43 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.8205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9864 Z= 0.305 Angle : 1.063 13.272 13384 Z= 0.527 Chirality : 0.056 0.273 1632 Planarity : 0.006 0.058 1652 Dihedral : 5.756 19.776 1316 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.18 % Allowed : 42.45 % Favored : 54.36 % 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: -0.26 (0.24), residues: 1244 helix: -0.27 (0.24), residues: 484 sheet: 0.15 (0.58), residues: 88 loop : 0.02 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 226 HIS 0.005 0.001 HIS C 180 PHE 0.021 0.004 PHE D 287 TYR 0.036 0.003 TYR B 171 ARG 0.011 0.002 ARG D 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5453.32 seconds wall clock time: 98 minutes 19.42 seconds (5899.42 seconds total)