Starting phenix.real_space_refine on Mon Nov 18 00:52:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/11_2024/8oi8_16888.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/11_2024/8oi8_16888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/11_2024/8oi8_16888.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/11_2024/8oi8_16888.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/11_2024/8oi8_16888.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oi8_16888/11_2024/8oi8_16888.cif" } resolution = 2.28 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= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 95 5.16 5 C 9050 2.51 5 N 2390 2.21 5 O 3345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14895 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.59, per 1000 atoms: 0.51 Number of scatterers: 14895 At special positions: 0 Unit cell: (92.435, 93.13, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 10 15.00 Mg 5 11.99 O 3345 8.00 N 2390 7.00 C 9050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 50.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.945A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.946A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.729A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.946A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.945A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.946A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.730A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 353 removed outlier: 6.279A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.274A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.274A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.380A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 4.418A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.588A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.380A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.499A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.588A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.379A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.379A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 733 hydrogen bonds defined for protein. 1863 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: 6.01 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4643 1.34 - 1.46: 2873 1.46 - 1.57: 6929 1.57 - 1.69: 15 1.69 - 1.81: 170 Bond restraints: 14630 Sorted by residual: bond pdb=" CG HIC C 73 " pdb=" ND1 HIC C 73 " ideal model delta sigma weight residual 1.370 1.312 0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" CG HIC E 73 " pdb=" ND1 HIC E 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" CG HIC B 73 " pdb=" ND1 HIC B 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.14e+00 bond pdb=" CG HIC D 73 " pdb=" ND1 HIC D 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CG HIC A 73 " pdb=" ND1 HIC A 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 19444 1.42 - 2.85: 235 2.85 - 4.27: 141 4.27 - 5.69: 20 5.69 - 7.11: 30 Bond angle restraints: 19870 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.47 109.91 3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 ... (remaining 19865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 8640 32.25 - 64.50: 110 64.50 - 96.76: 10 96.76 - 129.01: 0 129.01 - 161.26: 5 Dihedral angle restraints: 8765 sinusoidal: 3515 harmonic: 5250 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.77 161.22 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1261 0.031 - 0.062: 626 0.062 - 0.093: 189 0.093 - 0.124: 134 0.124 - 0.155: 5 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2212 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 243 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 243 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 243 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.017 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 112 2.42 - 3.04: 8768 3.04 - 3.66: 23764 3.66 - 4.28: 39834 4.28 - 4.90: 61663 Nonbonded interactions: 134141 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 507 " model vdw 1.798 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 512 " model vdw 1.819 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 541 " model vdw 1.824 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 525 " model vdw 1.827 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 530 " model vdw 1.836 2.170 ... (remaining 134136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 34.320 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.004 0.058 14630 Z= 0.275 Angle : 0.583 7.113 19870 Z= 0.280 Chirality : 0.044 0.155 2215 Planarity : 0.004 0.030 2525 Dihedral : 12.070 161.259 5395 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.65 % Allowed : 2.61 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.50 (0.19), residues: 1780 helix: -2.34 (0.14), residues: 755 sheet: -0.63 (0.26), residues: 325 loop : 0.86 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS E 88 PHE 0.009 0.001 PHE D 262 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.001 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 1.785 Fit side-chains REVERT: B 121 GLN cc_start: 0.8236 (tt0) cc_final: 0.8015 (tm-30) REVERT: B 211 ASP cc_start: 0.8004 (t70) cc_final: 0.7764 (t70) REVERT: D 44 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6789 (mpt) REVERT: D 276 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7023 (mt-10) REVERT: E 44 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6044 (mpt) outliers start: 10 outliers final: 0 residues processed: 249 average time/residue: 1.6394 time to fit residues: 442.9312 Evaluate side-chains 177 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain E residue 44 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 78 ASN B 12 ASN D 161 HIS D 225 GLN D 353 GLN E 12 ASN E 121 GLN E 225 GLN E 354 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14630 Z= 0.200 Angle : 0.617 7.372 19870 Z= 0.293 Chirality : 0.045 0.185 2215 Planarity : 0.004 0.034 2525 Dihedral : 9.408 138.847 2026 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.14 % Allowed : 6.14 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.20), residues: 1780 helix: -0.27 (0.18), residues: 740 sheet: 0.09 (0.26), residues: 330 loop : 2.04 (0.26), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.014 0.001 TYR A 143 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.772 Fit side-chains REVERT: C 72 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: C 171 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8615 (mp) REVERT: C 314 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: A 64 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.8837 (pp) REVERT: A 276 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7313 (mt-10) REVERT: D 44 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7174 (mpt) REVERT: D 125 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: D 286 ASP cc_start: 0.7641 (m-30) cc_final: 0.7401 (m-30) REVERT: E 44 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6703 (mpt) REVERT: E 64 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8544 (pp) REVERT: E 328 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8264 (tttt) outliers start: 48 outliers final: 7 residues processed: 216 average time/residue: 1.4178 time to fit residues: 335.6641 Evaluate side-chains 184 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 163 optimal weight: 0.4980 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 78 ASN A 225 GLN B 12 ASN D 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14630 Z= 0.202 Angle : 0.580 7.431 19870 Z= 0.277 Chirality : 0.044 0.184 2215 Planarity : 0.004 0.037 2525 Dihedral : 9.615 138.323 2026 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.20 % Allowed : 6.54 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1780 helix: 0.62 (0.19), residues: 745 sheet: 0.46 (0.26), residues: 330 loop : 2.25 (0.26), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS D 275 PHE 0.009 0.001 PHE D 262 TYR 0.014 0.001 TYR A 143 ARG 0.002 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 1.730 Fit side-chains REVERT: C 72 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: C 211 ASP cc_start: 0.7978 (t70) cc_final: 0.7773 (t70) REVERT: C 246 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: C 314 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: A 276 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: B 314 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: D 44 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7074 (mpt) REVERT: E 44 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.6569 (mpt) REVERT: E 64 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8564 (pp) REVERT: E 314 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: E 328 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8321 (tttt) outliers start: 49 outliers final: 13 residues processed: 202 average time/residue: 1.4665 time to fit residues: 324.3618 Evaluate side-chains 192 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14630 Z= 0.182 Angle : 0.564 7.272 19870 Z= 0.268 Chirality : 0.044 0.183 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.529 133.668 2026 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.20 % Allowed : 6.99 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.20), residues: 1780 helix: 0.98 (0.19), residues: 745 sheet: 0.55 (0.26), residues: 330 loop : 2.27 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS A 161 PHE 0.009 0.001 PHE D 262 TYR 0.013 0.001 TYR A 143 ARG 0.002 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.580 Fit side-chains REVERT: C 72 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: C 246 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: C 314 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: A 95 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7272 (mtm180) REVERT: A 276 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: B 95 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7497 (mtp180) REVERT: B 314 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: D 44 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7151 (mpt) REVERT: D 180 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8782 (tp) REVERT: E 41 GLN cc_start: 0.6607 (OUTLIER) cc_final: 0.6361 (pm20) REVERT: E 44 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.6617 (mpt) REVERT: E 64 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8577 (pp) REVERT: E 167 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: E 314 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8043 (tt0) outliers start: 49 outliers final: 14 residues processed: 207 average time/residue: 1.4666 time to fit residues: 332.0772 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 0.0570 chunk 148 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14630 Z= 0.202 Angle : 0.575 7.471 19870 Z= 0.274 Chirality : 0.045 0.184 2215 Planarity : 0.003 0.037 2525 Dihedral : 9.617 134.554 2026 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 3.01 % Allowed : 7.52 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.97 (0.20), residues: 1780 helix: 1.12 (0.20), residues: 745 sheet: 0.58 (0.26), residues: 330 loop : 2.26 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.005 0.001 HIS A 161 PHE 0.009 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.002 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.608 Fit side-chains REVERT: C 72 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: C 246 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7771 (tt0) REVERT: C 314 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: A 276 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: B 57 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7241 (pt0) REVERT: B 95 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7503 (mtp180) REVERT: B 125 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: B 314 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: D 44 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7092 (mpt) REVERT: D 180 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8772 (tp) REVERT: D 334 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7193 (pp20) REVERT: E 41 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: E 44 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.6572 (mpt) REVERT: E 64 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8582 (pp) REVERT: E 314 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8031 (tt0) outliers start: 46 outliers final: 15 residues processed: 199 average time/residue: 1.3982 time to fit residues: 305.4075 Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 161 HIS A 225 GLN B 12 ASN E 92 ASN E 161 HIS E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14630 Z= 0.321 Angle : 0.636 8.320 19870 Z= 0.308 Chirality : 0.048 0.196 2215 Planarity : 0.004 0.036 2525 Dihedral : 10.055 139.277 2026 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.14 % Allowed : 7.65 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.20), residues: 1780 helix: 1.05 (0.20), residues: 745 sheet: 0.56 (0.26), residues: 330 loop : 2.18 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.013 0.002 PHE D 262 TYR 0.014 0.001 TYR E 166 ARG 0.004 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 1.819 Fit side-chains REVERT: C 72 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: C 95 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7596 (mtm-85) REVERT: C 123 MET cc_start: 0.8919 (mmt) cc_final: 0.8689 (mmt) REVERT: C 246 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: C 314 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: A 276 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: B 57 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: B 95 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7497 (mtp180) REVERT: B 125 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: B 314 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: D 44 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.6959 (mpt) REVERT: D 180 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8847 (tp) REVERT: D 334 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: E 41 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6403 (pm20) REVERT: E 44 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6434 (mpt) REVERT: E 64 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8627 (pp) REVERT: E 99 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: E 132 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7808 (ttp) REVERT: E 314 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8053 (tt0) outliers start: 48 outliers final: 18 residues processed: 203 average time/residue: 1.4363 time to fit residues: 319.5160 Evaluate side-chains 205 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.0030 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 92 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14630 Z= 0.274 Angle : 0.615 8.024 19870 Z= 0.297 Chirality : 0.047 0.197 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.932 139.622 2026 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.88 % Allowed : 8.17 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.20), residues: 1780 helix: 1.10 (0.20), residues: 745 sheet: 0.59 (0.26), residues: 330 loop : 2.16 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.012 0.001 PHE D 262 TYR 0.012 0.001 TYR E 166 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 1.656 Fit side-chains REVERT: C 72 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: C 95 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7601 (mtm-85) REVERT: C 123 MET cc_start: 0.8913 (mmt) cc_final: 0.8627 (mmt) REVERT: C 246 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: C 314 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: A 276 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: B 57 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7217 (mt-10) REVERT: B 95 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7451 (mtp180) REVERT: B 125 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: B 314 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: D 44 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7039 (mpt) REVERT: D 180 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8834 (tp) REVERT: D 334 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7166 (pp20) REVERT: E 41 GLN cc_start: 0.6644 (OUTLIER) cc_final: 0.6373 (pm20) REVERT: E 44 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.6439 (mpt) REVERT: E 64 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8638 (pp) REVERT: E 99 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: E 314 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8037 (tt0) outliers start: 44 outliers final: 18 residues processed: 195 average time/residue: 1.4317 time to fit residues: 306.3165 Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 0.0070 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14630 Z= 0.165 Angle : 0.561 7.184 19870 Z= 0.267 Chirality : 0.044 0.182 2215 Planarity : 0.003 0.037 2525 Dihedral : 9.525 133.765 2026 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.42 % Allowed : 8.82 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.14 (0.20), residues: 1780 helix: 1.29 (0.20), residues: 740 sheet: 0.64 (0.26), residues: 330 loop : 2.31 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 PHE 0.009 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.002 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 1.521 Fit side-chains REVERT: C 72 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: C 314 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: A 276 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: B 95 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7453 (mtp180) REVERT: B 125 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: B 314 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: D 44 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7172 (mpt) REVERT: D 180 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8762 (tp) REVERT: E 41 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6319 (pm20) REVERT: E 44 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6484 (mpt) REVERT: E 64 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8568 (pp) REVERT: E 99 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: E 314 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8015 (tt0) outliers start: 37 outliers final: 12 residues processed: 193 average time/residue: 1.4174 time to fit residues: 299.7912 Evaluate side-chains 192 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 GLN B 12 ASN D 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14630 Z= 0.250 Angle : 0.601 7.874 19870 Z= 0.289 Chirality : 0.046 0.191 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.811 136.359 2026 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.29 % Allowed : 8.69 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.20), residues: 1780 helix: 1.20 (0.20), residues: 745 sheet: 0.66 (0.26), residues: 330 loop : 2.24 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS B 161 PHE 0.011 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 1.566 Fit side-chains REVERT: C 72 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: C 123 MET cc_start: 0.8911 (mmt) cc_final: 0.8578 (mmt) REVERT: C 314 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: A 276 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: B 57 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: B 95 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7458 (mtp180) REVERT: B 125 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: B 314 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8103 (tt0) REVERT: D 44 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7062 (mpt) REVERT: D 180 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8799 (tp) REVERT: E 41 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: E 44 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.6420 (mpt) REVERT: E 64 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8600 (pp) REVERT: E 99 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: E 314 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8040 (tt0) outliers start: 35 outliers final: 13 residues processed: 187 average time/residue: 1.4473 time to fit residues: 296.4330 Evaluate side-chains 192 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 0.0770 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 1.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 ASN D 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14630 Z= 0.205 Angle : 0.584 7.567 19870 Z= 0.279 Chirality : 0.045 0.188 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.666 134.947 2026 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.29 % Allowed : 8.76 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.20), residues: 1780 helix: 1.23 (0.20), residues: 745 sheet: 0.64 (0.26), residues: 330 loop : 2.25 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 PHE 0.010 0.001 PHE D 262 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG B 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.763 Fit side-chains REVERT: C 72 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: C 95 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7602 (mtm-85) REVERT: C 123 MET cc_start: 0.8911 (mmt) cc_final: 0.8580 (mmt) REVERT: C 246 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: C 314 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: A 276 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: B 57 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: B 95 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7460 (mtp180) REVERT: B 125 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: B 314 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: D 44 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7102 (mpt) REVERT: D 180 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8778 (tp) REVERT: E 41 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: E 44 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6417 (mpt) REVERT: E 64 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8582 (pp) REVERT: E 99 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: E 314 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8031 (tt0) outliers start: 35 outliers final: 14 residues processed: 185 average time/residue: 1.4682 time to fit residues: 297.4881 Evaluate side-chains 196 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 GLN B 12 ASN D 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.084760 restraints weight = 15580.939| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.31 r_work: 0.2805 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14630 Z= 0.321 Angle : 0.640 8.259 19870 Z= 0.310 Chirality : 0.048 0.196 2215 Planarity : 0.004 0.035 2525 Dihedral : 10.054 139.084 2026 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.55 % Allowed : 8.43 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.95 (0.20), residues: 1780 helix: 1.13 (0.20), residues: 745 sheet: 0.63 (0.26), residues: 330 loop : 2.18 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.005 0.001 HIS B 161 PHE 0.013 0.002 PHE D 262 TYR 0.009 0.001 TYR A 143 ARG 0.004 0.000 ARG D 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.44 seconds wall clock time: 105 minutes 19.64 seconds (6319.64 seconds total)