Starting phenix.real_space_refine on Sat Sep 12 08:54:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2026/6t25_10367.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.012 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 9200 2.51 5 N 2460 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14590 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2835 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} 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: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 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} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.48, per 1000 atoms: 0.17 Number of scatterers: 14590 At special positions: 0 Unit cell: (96.32, 92.96, 188.16, 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 2820 8.00 N 2460 7.00 C 9200 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 Links applied TRANS " TRP F 1 " - " ALA F 7 " " DTH F 4 " - " ALA F 3 " " TRP G 1 " - " ALA G 7 " " DTH G 4 " - " ALA G 3 " " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 504.8 milliseconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 54.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 78 through 93 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.540A 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 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 234 through 237 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 306 removed outlier: 3.573A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) 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 349 Processing helix chain 'A' and resid 350 through 356 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 62 Processing helix chain 'B' and resid 78 through 93 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.540A 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 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 234 through 237 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 306 removed outlier: 3.573A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) 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 349 Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 93 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.540A 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 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 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 306 removed outlier: 3.573A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) 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 349 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 62 Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 124 removed outlier: 3.540A 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 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 234 through 237 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 306 removed outlier: 3.573A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) 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 349 Processing helix chain 'D' and resid 350 through 356 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 62 Processing helix chain 'E' and resid 78 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 124 removed outlier: 3.540A 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 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 234 through 237 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 306 removed outlier: 3.573A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) 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 349 Processing helix chain 'E' and resid 350 through 356 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 'A' and resid 29 through 32 removed outlier: 4.005A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.136A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.004A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.137A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.005A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.136A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.005A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN D 12 " --> 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: 6.136A pdb=" N ASN 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: 4.005A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN E 12 " --> 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: 6.137A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 800 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3600 1.32 - 1.44: 3587 1.44 - 1.57: 7553 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 14905 Sorted by residual: bond pdb=" CA EEP F 2 " pdb=" C EEP F 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" CA ILE E 192 " pdb=" CB ILE E 192 " ideal model delta sigma weight residual 1.540 1.480 0.059 1.29e-02 6.01e+03 2.12e+01 bond pdb=" CA EEP G 2 " pdb=" C EEP G 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.480 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 14900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 17401 2.04 - 4.07: 2258 4.07 - 6.11: 418 6.11 - 8.14: 133 8.14 - 10.18: 30 Bond angle restraints: 20240 Sorted by residual: angle pdb=" C GLY B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.47 129.65 -10.18 1.16e+00 7.43e-01 7.70e+01 angle pdb=" C GLY C 366 " pdb=" N PRO C 367 " pdb=" CA PRO C 367 " ideal model delta sigma weight residual 119.47 129.64 -10.17 1.16e+00 7.43e-01 7.69e+01 angle pdb=" C GLY D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.47 129.63 -10.16 1.16e+00 7.43e-01 7.67e+01 angle pdb=" C GLY E 366 " pdb=" N PRO E 367 " pdb=" CA PRO E 367 " ideal model delta sigma weight residual 119.47 129.60 -10.13 1.16e+00 7.43e-01 7.62e+01 angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.47 129.59 -10.12 1.16e+00 7.43e-01 7.61e+01 ... (remaining 20235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.11: 8790 30.11 - 60.21: 105 60.21 - 90.32: 30 90.32 - 120.42: 0 120.42 - 150.53: 10 Dihedral angle restraints: 8935 sinusoidal: 3600 harmonic: 5335 Sorted by residual: dihedral pdb=" O1B ADP E 376 " pdb=" O3A ADP E 376 " pdb=" PB ADP E 376 " pdb=" PA ADP E 376 " ideal model delta sinusoidal sigma weight residual -60.00 90.53 -150.53 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 90.49 -150.49 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O1B ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PB ADP A 376 " pdb=" PA ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 90.47 -150.48 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 8932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 2250 1.032 - 2.064: 0 2.064 - 3.096: 0 3.096 - 4.127: 0 4.127 - 5.159: 10 Chirality restraints: 2260 Sorted by residual: chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.63 5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" CA DTH F 4 " pdb=" N DTH F 4 " pdb=" C DTH F 4 " pdb=" CB DTH F 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.63 5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" CA DTH G 4 " pdb=" N DTH G 4 " pdb=" C DTH G 4 " pdb=" CB DTH G 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.63 5.16 2.00e-01 2.50e+01 6.65e+02 ... (remaining 2257 not shown) Planarity restraints: 2575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 340 " 0.030 2.00e-02 2.50e+03 1.52e-02 5.75e+00 pdb=" CG TRP B 340 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 340 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 340 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 340 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 340 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 340 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 340 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 340 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 69 " 0.032 2.00e-02 2.50e+03 1.69e-02 5.74e+00 pdb=" CG TYR A 69 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 69 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 69 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 69 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 69 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 69 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 69 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 69 " 0.031 2.00e-02 2.50e+03 1.69e-02 5.71e+00 pdb=" CG TYR C 69 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR C 69 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 69 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 69 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 69 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 69 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 69 " 0.025 2.00e-02 2.50e+03 ... (remaining 2572 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 30 2.37 - 3.01: 9804 3.01 - 3.64: 21248 3.64 - 4.27: 34850 4.27 - 4.90: 56463 Nonbonded interactions: 122395 Sorted by model distance: nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.742 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.743 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.743 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.743 3.620 nonbonded pdb=" CD1 TRP F 1 " pdb=" SG CYS F 5 " model vdw 1.743 3.620 ... (remaining 122390 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.018 0.092 14915 Z= 1.166 Angle : 1.597 10.178 20270 Z= 1.068 Chirality : 0.353 5.159 2260 Planarity : 0.006 0.046 2565 Dihedral : 12.031 150.531 5485 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.32 % Allowed : 0.00 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 1775 helix: -0.97 (0.16), residues: 820 sheet: -0.76 (0.26), residues: 320 loop : 0.32 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 183 TYR 0.032 0.006 TYR A 69 PHE 0.011 0.003 PHE B 262 TRP 0.030 0.008 TRP B 340 HIS 0.006 0.002 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.01829 / 1.17 (14905) covalent geometry : angle 1.59072 / 1.07 (20240) hydrogen bonds : bond 0.18642 / 12.45 ( 790) hydrogen bonds : angle 7.65629 / 5.45 ( 1995) link_TRANS : bond 0.00767 / 0.46 ( 10) link_TRANS : angle 4.11582 / 2.79 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 512 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ASN cc_start: 0.8253 (m-40) cc_final: 0.8001 (t0) REVERT: A 316 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8124 (mm-30) REVERT: A 372 ARG cc_start: 0.6226 (ttp-170) cc_final: 0.5972 (ttp-170) REVERT: B 34 ILE cc_start: 0.8755 (mt) cc_final: 0.8508 (pt) REVERT: B 59 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6824 (mm-40) REVERT: B 151 ILE cc_start: 0.8592 (mt) cc_final: 0.8257 (tt) REVERT: B 202 THR cc_start: 0.7519 (p) cc_final: 0.6809 (p) REVERT: B 325 MET cc_start: 0.7814 (mmm) cc_final: 0.7464 (mmt) REVERT: C 143 TYR cc_start: 0.8430 (m-80) cc_final: 0.8118 (m-10) REVERT: C 227 MET cc_start: 0.8113 (mmm) cc_final: 0.7719 (tpp) REVERT: D 11 ASP cc_start: 0.8202 (t0) cc_final: 0.7944 (t0) REVERT: D 117 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7334 (tm-30) REVERT: D 202 THR cc_start: 0.7912 (p) cc_final: 0.7086 (p) REVERT: D 222 ASP cc_start: 0.8283 (t0) cc_final: 0.7516 (p0) REVERT: D 324 THR cc_start: 0.8293 (p) cc_final: 0.8023 (p) REVERT: E 34 ILE cc_start: 0.9196 (mt) cc_final: 0.8907 (pt) REVERT: E 78 ASN cc_start: 0.7580 (t0) cc_final: 0.6962 (m-40) REVERT: E 93 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6379 (mm-30) REVERT: G 5 CYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6273 (p) outliers start: 5 outliers final: 0 residues processed: 517 average time/residue: 0.1237 time to fit residues: 94.5629 Evaluate side-chains 235 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS D 88 HIS D 92 ASN D 173 HIS D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.113535 restraints weight = 20276.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116552 restraints weight = 11652.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.118599 restraints weight = 7453.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119999 restraints weight = 5120.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120984 restraints weight = 3726.084| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14915 Z= 0.149 Angle : 0.687 7.294 20270 Z= 0.339 Chirality : 0.049 0.357 2260 Planarity : 0.005 0.034 2565 Dihedral : 11.671 148.907 2066 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.08 % Allowed : 9.68 % Favored : 88.25 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1775 helix: 0.93 (0.18), residues: 785 sheet: -0.37 (0.27), residues: 315 loop : 1.22 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.018 0.001 TYR E 53 PHE 0.012 0.001 PHE A 124 TRP 0.013 0.002 TRP J 1 HIS 0.007 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (14905) covalent geometry : angle 0.68500 / 0.34 (20240) hydrogen bonds : bond 0.04012 / 2.71 ( 790) hydrogen bonds : angle 5.27854 / 3.80 ( 1995) link_TRANS : bond 0.00174 / 0.11 ( 10) link_TRANS : angle 1.54480 / 0.85 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 332 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9297 (t) cc_final: 0.8851 (m) REVERT: A 113 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.6190 (mmtt) REVERT: A 176 MET cc_start: 0.7163 (mmp) cc_final: 0.6560 (mmt) REVERT: A 279 TYR cc_start: 0.8635 (t80) cc_final: 0.8389 (t80) REVERT: A 313 MET cc_start: 0.8025 (tpp) cc_final: 0.7808 (ttm) REVERT: A 325 MET cc_start: 0.7111 (mmp) cc_final: 0.6763 (tpp) REVERT: B 88 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6377 (t-90) REVERT: B 210 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7099 (ttm170) REVERT: C 57 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7056 (mt-10) REVERT: C 162 ASN cc_start: 0.8166 (t0) cc_final: 0.7882 (t0) REVERT: D 117 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6958 (tm-30) REVERT: D 143 TYR cc_start: 0.7229 (m-80) cc_final: 0.6645 (m-80) REVERT: D 162 ASN cc_start: 0.7809 (t0) cc_final: 0.7492 (t0) REVERT: D 176 MET cc_start: 0.7102 (mmp) cc_final: 0.6834 (mmt) REVERT: D 283 MET cc_start: 0.7936 (mmp) cc_final: 0.7470 (mmm) REVERT: E 72 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7080 (mp0) REVERT: E 93 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6421 (mm-30) REVERT: E 119 MET cc_start: 0.8319 (ttm) cc_final: 0.8098 (ttm) REVERT: E 189 LEU cc_start: 0.8542 (tp) cc_final: 0.8338 (tp) REVERT: E 217 CYS cc_start: 0.7333 (m) cc_final: 0.6768 (m) REVERT: E 238 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8067 (mtpt) REVERT: E 259 GLU cc_start: 0.8672 (tp30) cc_final: 0.8376 (tp30) REVERT: E 311 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: E 316 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7717 (mm-30) REVERT: E 363 ASP cc_start: 0.6983 (t0) cc_final: 0.5667 (p0) outliers start: 32 outliers final: 18 residues processed: 355 average time/residue: 0.1113 time to fit residues: 60.2252 Evaluate side-chains 265 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 311 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 246 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 297 ASN D 88 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109500 restraints weight = 20613.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112346 restraints weight = 12013.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114318 restraints weight = 7777.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115675 restraints weight = 5386.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116631 restraints weight = 3950.218| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14915 Z= 0.147 Angle : 0.644 7.263 20270 Z= 0.314 Chirality : 0.049 0.414 2260 Planarity : 0.004 0.034 2565 Dihedral : 11.225 142.483 2065 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.47 % Allowed : 13.05 % Favored : 84.48 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1775 helix: 1.29 (0.19), residues: 785 sheet: -0.11 (0.26), residues: 345 loop : 1.46 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.015 0.001 TYR D 218 PHE 0.017 0.001 PHE D 352 TRP 0.011 0.001 TRP D 340 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (14905) covalent geometry : angle 0.64238 / 0.31 (20240) hydrogen bonds : bond 0.03602 / 2.43 ( 790) hydrogen bonds : angle 4.95132 / 3.57 ( 1995) link_TRANS : bond 0.00278 / 0.17 ( 10) link_TRANS : angle 1.30329 / 0.71 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9411 (t) cc_final: 0.8977 (m) REVERT: A 113 LYS cc_start: 0.8003 (mmtm) cc_final: 0.6698 (mptt) REVERT: A 143 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: A 176 MET cc_start: 0.7209 (mmp) cc_final: 0.6720 (mmt) REVERT: A 279 TYR cc_start: 0.8707 (t80) cc_final: 0.8433 (t80) REVERT: A 313 MET cc_start: 0.8208 (tpp) cc_final: 0.7850 (ttm) REVERT: A 325 MET cc_start: 0.7420 (mmp) cc_final: 0.7114 (tpp) REVERT: B 81 ASP cc_start: 0.6879 (m-30) cc_final: 0.6601 (m-30) REVERT: B 88 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6152 (t-90) REVERT: C 57 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7250 (mt-10) REVERT: C 121 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 325 MET cc_start: 0.7668 (tpp) cc_final: 0.7147 (tpp) REVERT: C 328 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8078 (ttmm) REVERT: D 117 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6990 (tm-30) REVERT: D 143 TYR cc_start: 0.7271 (m-80) cc_final: 0.6951 (m-80) REVERT: D 162 ASN cc_start: 0.7923 (t0) cc_final: 0.7625 (t0) REVERT: D 176 MET cc_start: 0.7103 (mmp) cc_final: 0.6787 (mmt) REVERT: D 292 ASP cc_start: 0.8029 (t0) cc_final: 0.7782 (t0) REVERT: D 299 MET cc_start: 0.8213 (mtp) cc_final: 0.7949 (mmm) REVERT: D 313 MET cc_start: 0.8087 (ttm) cc_final: 0.7543 (ttm) REVERT: D 334 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6519 (tp30) REVERT: E 50 LYS cc_start: 0.8447 (mttt) cc_final: 0.8169 (mtpp) REVERT: E 68 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8079 (mmtt) REVERT: E 123 MET cc_start: 0.8161 (tpp) cc_final: 0.7731 (tpt) REVERT: E 217 CYS cc_start: 0.7600 (m) cc_final: 0.7042 (m) REVERT: E 225 ASN cc_start: 0.8455 (m110) cc_final: 0.8194 (m110) REVERT: E 259 GLU cc_start: 0.8758 (tp30) cc_final: 0.8457 (tp30) REVERT: E 316 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7652 (mm-30) outliers start: 38 outliers final: 23 residues processed: 321 average time/residue: 0.1079 time to fit residues: 53.5278 Evaluate side-chains 258 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 149 optimal weight: 0.0870 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 121 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 88 HIS D 263 GLN E 296 ASN E 297 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105865 restraints weight = 20956.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108627 restraints weight = 12328.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110509 restraints weight = 8013.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111860 restraints weight = 5604.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.112812 restraints weight = 4116.879| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14915 Z= 0.180 Angle : 0.666 10.511 20270 Z= 0.323 Chirality : 0.050 0.409 2260 Planarity : 0.005 0.036 2565 Dihedral : 10.971 140.086 2065 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.86 % Allowed : 14.35 % Favored : 82.79 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1775 helix: 1.20 (0.19), residues: 785 sheet: -0.13 (0.26), residues: 345 loop : 1.32 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.013 0.001 TYR E 69 PHE 0.010 0.001 PHE D 352 TRP 0.014 0.002 TRP D 340 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (14905) covalent geometry : angle 0.66476 / 0.32 (20240) hydrogen bonds : bond 0.03711 / 2.50 ( 790) hydrogen bonds : angle 4.96441 / 3.56 ( 1995) link_TRANS : bond 0.00229 / 0.14 ( 10) link_TRANS : angle 1.36241 / 0.73 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7847 (mttm) cc_final: 0.6744 (mptt) REVERT: A 176 MET cc_start: 0.7164 (mmp) cc_final: 0.6876 (mmt) REVERT: A 313 MET cc_start: 0.8395 (tpp) cc_final: 0.7895 (ttm) REVERT: A 325 MET cc_start: 0.7831 (mmp) cc_final: 0.7421 (mmt) REVERT: C 121 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 316 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7208 (mm-30) REVERT: D 88 HIS cc_start: 0.7543 (t70) cc_final: 0.7306 (t-90) REVERT: D 117 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6977 (tm-30) REVERT: D 123 MET cc_start: 0.8022 (tpp) cc_final: 0.7789 (tpt) REVERT: D 143 TYR cc_start: 0.7360 (m-80) cc_final: 0.6827 (m-80) REVERT: D 162 ASN cc_start: 0.7996 (t0) cc_final: 0.7661 (t0) REVERT: D 283 MET cc_start: 0.8318 (mmm) cc_final: 0.8024 (mmp) REVERT: D 292 ASP cc_start: 0.7978 (t0) cc_final: 0.7771 (t0) REVERT: D 299 MET cc_start: 0.8215 (mtp) cc_final: 0.7875 (mtp) REVERT: D 313 MET cc_start: 0.8005 (ttm) cc_final: 0.7536 (ttm) REVERT: D 334 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6692 (tp30) REVERT: E 68 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8066 (mmtt) REVERT: E 217 CYS cc_start: 0.7954 (m) cc_final: 0.7647 (m) REVERT: E 316 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7693 (mm-30) outliers start: 44 outliers final: 31 residues processed: 290 average time/residue: 0.1055 time to fit residues: 47.9213 Evaluate side-chains 253 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 41 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 chunk 13 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.099145 restraints weight = 21604.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102380 restraints weight = 11971.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.104570 restraints weight = 7480.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106096 restraints weight = 5093.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107177 restraints weight = 3684.097| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14915 Z= 0.142 Angle : 0.628 7.099 20270 Z= 0.301 Chirality : 0.049 0.367 2260 Planarity : 0.004 0.035 2565 Dihedral : 10.497 133.806 2065 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.79 % Allowed : 15.45 % Favored : 81.75 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1775 helix: 1.26 (0.19), residues: 785 sheet: -0.10 (0.27), residues: 345 loop : 1.20 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 147 TYR 0.011 0.001 TYR C 198 PHE 0.010 0.001 PHE D 352 TRP 0.013 0.002 TRP D 340 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14905) covalent geometry : angle 0.62636 / 0.30 (20240) hydrogen bonds : bond 0.03275 / 2.22 ( 790) hydrogen bonds : angle 4.84419 / 3.48 ( 1995) link_TRANS : bond 0.00257 / 0.16 ( 10) link_TRANS : angle 1.34154 / 0.73 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7851 (mttm) cc_final: 0.6305 (mptt) REVERT: A 117 GLU cc_start: 0.7740 (mp0) cc_final: 0.6762 (mp0) REVERT: A 176 MET cc_start: 0.7397 (mmp) cc_final: 0.7063 (mmt) REVERT: A 192 ILE cc_start: 0.8672 (mm) cc_final: 0.8381 (mm) REVERT: A 313 MET cc_start: 0.8438 (tpp) cc_final: 0.7899 (ttm) REVERT: A 325 MET cc_start: 0.8313 (mmp) cc_final: 0.7774 (mmt) REVERT: B 57 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7448 (mp0) REVERT: B 81 ASP cc_start: 0.7405 (m-30) cc_final: 0.7106 (m-30) REVERT: C 316 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 334 GLU cc_start: 0.8122 (pt0) cc_final: 0.7885 (pp20) REVERT: D 88 HIS cc_start: 0.7654 (t70) cc_final: 0.7399 (t70) REVERT: D 117 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6714 (tm-30) REVERT: D 123 MET cc_start: 0.8295 (tpp) cc_final: 0.7999 (tpt) REVERT: D 143 TYR cc_start: 0.7313 (m-80) cc_final: 0.6876 (m-80) REVERT: D 162 ASN cc_start: 0.8098 (t0) cc_final: 0.7720 (t0) REVERT: D 176 MET cc_start: 0.7364 (tpp) cc_final: 0.7129 (mtt) REVERT: D 237 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: D 283 MET cc_start: 0.8271 (mmm) cc_final: 0.7870 (mmm) REVERT: D 292 ASP cc_start: 0.8090 (t0) cc_final: 0.7731 (t0) REVERT: D 299 MET cc_start: 0.8315 (mtp) cc_final: 0.7601 (mtp) REVERT: D 305 MET cc_start: 0.7247 (mmm) cc_final: 0.7004 (mmm) REVERT: D 313 MET cc_start: 0.8059 (ttm) cc_final: 0.7702 (ttm) REVERT: E 57 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7656 (mp0) REVERT: E 68 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7995 (mmtt) REVERT: E 224 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 226 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8181 (mm-30) REVERT: E 244 ASP cc_start: 0.7571 (p0) cc_final: 0.7366 (t0) REVERT: E 283 MET cc_start: 0.7025 (mmp) cc_final: 0.6654 (mmm) REVERT: E 303 THR cc_start: 0.8762 (p) cc_final: 0.8461 (t) REVERT: E 316 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7572 (mm-30) outliers start: 43 outliers final: 34 residues processed: 273 average time/residue: 0.1097 time to fit residues: 46.4343 Evaluate side-chains 260 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 27 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100006 restraints weight = 21399.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103245 restraints weight = 11865.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105406 restraints weight = 7425.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.106915 restraints weight = 5055.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.108029 restraints weight = 3669.008| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14915 Z= 0.128 Angle : 0.604 7.099 20270 Z= 0.288 Chirality : 0.048 0.346 2260 Planarity : 0.004 0.035 2565 Dihedral : 9.988 126.945 2065 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.66 % Allowed : 16.10 % Favored : 81.23 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.20), residues: 1775 helix: 1.56 (0.19), residues: 755 sheet: -0.05 (0.27), residues: 345 loop : 1.21 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 95 TYR 0.009 0.001 TYR C 198 PHE 0.011 0.001 PHE D 352 TRP 0.013 0.001 TRP D 340 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14905) covalent geometry : angle 0.60254 / 0.29 (20240) hydrogen bonds : bond 0.03105 / 2.10 ( 790) hydrogen bonds : angle 4.76466 / 3.42 ( 1995) link_TRANS : bond 0.00254 / 0.16 ( 10) link_TRANS : angle 1.36605 / 0.75 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7715 (mttm) cc_final: 0.6035 (mptt) REVERT: A 117 GLU cc_start: 0.7706 (mp0) cc_final: 0.6607 (mp0) REVERT: A 176 MET cc_start: 0.7429 (mmp) cc_final: 0.7047 (mmt) REVERT: A 283 MET cc_start: 0.7604 (mmm) cc_final: 0.7297 (mmm) REVERT: A 303 THR cc_start: 0.8682 (p) cc_final: 0.8306 (t) REVERT: A 313 MET cc_start: 0.8498 (tpp) cc_final: 0.7951 (ttm) REVERT: A 325 MET cc_start: 0.8441 (mmp) cc_final: 0.7965 (mmt) REVERT: B 57 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7464 (mp0) REVERT: B 81 ASP cc_start: 0.7402 (m-30) cc_final: 0.7081 (m-30) REVERT: C 316 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7037 (mm-30) REVERT: C 334 GLU cc_start: 0.8066 (pt0) cc_final: 0.7813 (pp20) REVERT: D 88 HIS cc_start: 0.7657 (t70) cc_final: 0.7424 (t70) REVERT: D 100 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6438 (mp0) REVERT: D 117 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6722 (tm-30) REVERT: D 123 MET cc_start: 0.8387 (tpp) cc_final: 0.8119 (tpt) REVERT: D 143 TYR cc_start: 0.7294 (m-80) cc_final: 0.6859 (m-80) REVERT: D 162 ASN cc_start: 0.8057 (t0) cc_final: 0.7676 (t0) REVERT: D 176 MET cc_start: 0.7335 (tpp) cc_final: 0.7040 (mtt) REVERT: D 237 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: D 283 MET cc_start: 0.8147 (mmm) cc_final: 0.7767 (mmm) REVERT: D 292 ASP cc_start: 0.8151 (t0) cc_final: 0.7818 (t0) REVERT: D 299 MET cc_start: 0.8312 (mtp) cc_final: 0.7589 (mtp) REVERT: D 305 MET cc_start: 0.7272 (mmm) cc_final: 0.7056 (mmm) REVERT: D 313 MET cc_start: 0.8035 (ttm) cc_final: 0.7682 (ttm) REVERT: D 334 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: E 57 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7696 (mp0) REVERT: E 68 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7918 (mmtt) REVERT: E 96 VAL cc_start: 0.8318 (p) cc_final: 0.8033 (m) REVERT: E 224 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7536 (tm-30) REVERT: E 226 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8230 (mm-30) REVERT: E 283 MET cc_start: 0.7093 (mmp) cc_final: 0.6777 (mmm) REVERT: E 303 THR cc_start: 0.8811 (p) cc_final: 0.8475 (t) REVERT: E 316 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7543 (mm-30) outliers start: 41 outliers final: 35 residues processed: 263 average time/residue: 0.1024 time to fit residues: 42.5059 Evaluate side-chains 255 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100608 restraints weight = 21306.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.103839 restraints weight = 11762.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.106018 restraints weight = 7348.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107546 restraints weight = 4995.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.108606 restraints weight = 3608.051| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14915 Z= 0.121 Angle : 0.598 8.731 20270 Z= 0.283 Chirality : 0.047 0.329 2260 Planarity : 0.004 0.036 2565 Dihedral : 9.372 117.277 2065 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.60 % Allowed : 16.69 % Favored : 80.71 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.20), residues: 1775 helix: 1.59 (0.19), residues: 755 sheet: -0.03 (0.27), residues: 345 loop : 1.21 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 95 TYR 0.008 0.001 TYR C 198 PHE 0.012 0.001 PHE D 352 TRP 0.012 0.001 TRP D 340 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14905) covalent geometry : angle 0.59608 / 0.28 (20240) hydrogen bonds : bond 0.02993 / 2.03 ( 790) hydrogen bonds : angle 4.70355 / 3.36 ( 1995) link_TRANS : bond 0.00258 / 0.16 ( 10) link_TRANS : angle 1.33943 / 0.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7801 (mttm) cc_final: 0.6392 (mptt) REVERT: A 117 GLU cc_start: 0.7702 (mp0) cc_final: 0.6972 (mp0) REVERT: A 176 MET cc_start: 0.7475 (mmp) cc_final: 0.7019 (mmt) REVERT: A 303 THR cc_start: 0.8731 (p) cc_final: 0.8427 (t) REVERT: A 313 MET cc_start: 0.8483 (tpp) cc_final: 0.7928 (ttm) REVERT: A 325 MET cc_start: 0.8510 (mmp) cc_final: 0.8096 (mmt) REVERT: B 57 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7338 (mp0) REVERT: B 81 ASP cc_start: 0.7415 (m-30) cc_final: 0.7078 (m-30) REVERT: C 121 GLN cc_start: 0.8251 (tm-30) cc_final: 0.6977 (tt0) REVERT: C 316 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7118 (mm-30) REVERT: C 334 GLU cc_start: 0.8105 (pt0) cc_final: 0.7845 (pp20) REVERT: C 369 ILE cc_start: 0.8720 (tt) cc_final: 0.8444 (pt) REVERT: D 100 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6471 (mp0) REVERT: D 117 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6658 (tm-30) REVERT: D 123 MET cc_start: 0.8331 (tpp) cc_final: 0.8090 (tpt) REVERT: D 143 TYR cc_start: 0.7291 (m-80) cc_final: 0.6882 (m-80) REVERT: D 162 ASN cc_start: 0.8023 (t0) cc_final: 0.7632 (t0) REVERT: D 176 MET cc_start: 0.7277 (tpp) cc_final: 0.6998 (mtt) REVERT: D 237 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: D 283 MET cc_start: 0.8087 (mmm) cc_final: 0.7740 (mmm) REVERT: D 292 ASP cc_start: 0.8139 (t0) cc_final: 0.7804 (t0) REVERT: D 299 MET cc_start: 0.8264 (mtp) cc_final: 0.7773 (mtp) REVERT: D 305 MET cc_start: 0.7272 (mmm) cc_final: 0.6990 (tmm) REVERT: D 313 MET cc_start: 0.8036 (ttm) cc_final: 0.7711 (ttm) REVERT: D 316 GLU cc_start: 0.7463 (mp0) cc_final: 0.7236 (mp0) REVERT: D 334 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: E 57 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7758 (mp0) REVERT: E 68 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7900 (mmtt) REVERT: E 96 VAL cc_start: 0.8163 (p) cc_final: 0.7896 (m) REVERT: E 224 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7488 (tm-30) REVERT: E 283 MET cc_start: 0.7174 (mmp) cc_final: 0.6914 (mmm) REVERT: E 303 THR cc_start: 0.8816 (p) cc_final: 0.8529 (t) REVERT: E 316 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7559 (mm-30) REVERT: E 372 ARG cc_start: 0.6104 (mtp180) cc_final: 0.5710 (mtp180) outliers start: 40 outliers final: 34 residues processed: 265 average time/residue: 0.1012 time to fit residues: 42.4652 Evaluate side-chains 262 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 292 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 81 optimal weight: 0.0670 chunk 150 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 69 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN D 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.114934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.102113 restraints weight = 21327.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105366 restraints weight = 11699.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107571 restraints weight = 7281.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109117 restraints weight = 4930.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110177 restraints weight = 3542.365| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14915 Z= 0.108 Angle : 0.593 8.827 20270 Z= 0.280 Chirality : 0.047 0.331 2260 Planarity : 0.004 0.036 2565 Dihedral : 8.751 116.858 2065 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.08 % Allowed : 17.66 % Favored : 80.26 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.20), residues: 1775 helix: 1.68 (0.19), residues: 755 sheet: 0.01 (0.27), residues: 345 loop : 1.22 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.008 0.001 TYR E 306 PHE 0.013 0.001 PHE D 352 TRP 0.012 0.001 TRP D 340 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (14905) covalent geometry : angle 0.59083 / 0.28 (20240) hydrogen bonds : bond 0.02849 / 1.94 ( 790) hydrogen bonds : angle 4.62907 / 3.31 ( 1995) link_TRANS : bond 0.00281 / 0.18 ( 10) link_TRANS : angle 1.34311 / 0.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7906 (mttm) cc_final: 0.6354 (mptt) REVERT: A 117 GLU cc_start: 0.7725 (mt-10) cc_final: 0.6970 (mp0) REVERT: A 176 MET cc_start: 0.7476 (mmp) cc_final: 0.7013 (mmt) REVERT: A 283 MET cc_start: 0.7545 (mmm) cc_final: 0.7280 (mmm) REVERT: A 303 THR cc_start: 0.8703 (p) cc_final: 0.8476 (t) REVERT: A 313 MET cc_start: 0.8474 (tpp) cc_final: 0.7911 (ttm) REVERT: A 325 MET cc_start: 0.8504 (mmp) cc_final: 0.8103 (mmt) REVERT: B 51 ASP cc_start: 0.7803 (m-30) cc_final: 0.7545 (t0) REVERT: B 57 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7347 (mp0) REVERT: B 81 ASP cc_start: 0.7396 (m-30) cc_final: 0.7112 (m-30) REVERT: B 87 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6950 (t-90) REVERT: C 121 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7019 (tt0) REVERT: C 316 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7097 (mm-30) REVERT: C 334 GLU cc_start: 0.8101 (pt0) cc_final: 0.7833 (pp20) REVERT: C 369 ILE cc_start: 0.8516 (tt) cc_final: 0.8238 (pt) REVERT: D 117 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6634 (tm-30) REVERT: D 123 MET cc_start: 0.8285 (tpp) cc_final: 0.8045 (tpt) REVERT: D 162 ASN cc_start: 0.8063 (t0) cc_final: 0.7649 (t0) REVERT: D 176 MET cc_start: 0.7251 (tpp) cc_final: 0.6999 (mtt) REVERT: D 237 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: D 271 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 283 MET cc_start: 0.8091 (mmm) cc_final: 0.7755 (mmm) REVERT: D 292 ASP cc_start: 0.8124 (t0) cc_final: 0.7789 (t0) REVERT: D 299 MET cc_start: 0.8266 (mtp) cc_final: 0.7550 (mtp) REVERT: D 305 MET cc_start: 0.7193 (mmm) cc_final: 0.6911 (tmm) REVERT: D 313 MET cc_start: 0.8031 (ttm) cc_final: 0.7713 (ttm) REVERT: D 316 GLU cc_start: 0.7457 (mp0) cc_final: 0.7106 (mp0) REVERT: E 57 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7753 (mp0) REVERT: E 68 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7910 (mmtt) REVERT: E 96 VAL cc_start: 0.8307 (p) cc_final: 0.8019 (m) REVERT: E 123 MET cc_start: 0.7843 (tpp) cc_final: 0.7434 (tpt) REVERT: E 224 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7458 (tm-30) REVERT: E 271 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8010 (p) REVERT: E 283 MET cc_start: 0.7099 (mmp) cc_final: 0.6865 (mmm) REVERT: E 303 THR cc_start: 0.8733 (p) cc_final: 0.8466 (t) REVERT: E 316 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7494 (mm-30) outliers start: 32 outliers final: 26 residues processed: 271 average time/residue: 0.0982 time to fit residues: 42.2384 Evaluate side-chains 268 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 51 optimal weight: 0.0770 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097986 restraints weight = 21720.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101155 restraints weight = 12126.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103284 restraints weight = 7623.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104794 restraints weight = 5225.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105849 restraints weight = 3800.353| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14915 Z= 0.176 Angle : 0.644 7.770 20270 Z= 0.309 Chirality : 0.049 0.347 2260 Planarity : 0.004 0.038 2565 Dihedral : 8.758 111.893 2065 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.40 % Allowed : 17.79 % Favored : 79.81 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1775 helix: 1.51 (0.19), residues: 755 sheet: -0.10 (0.27), residues: 345 loop : 1.12 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 147 TYR 0.011 0.001 TYR E 69 PHE 0.015 0.001 PHE D 352 TRP 0.011 0.002 TRP B 340 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (14905) covalent geometry : angle 0.64202 / 0.31 (20240) hydrogen bonds : bond 0.03495 / 2.35 ( 790) hydrogen bonds : angle 4.80605 / 3.43 ( 1995) link_TRANS : bond 0.00191 / 0.12 ( 10) link_TRANS : angle 1.34651 / 0.74 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7909 (mttm) cc_final: 0.6353 (mptt) REVERT: A 117 GLU cc_start: 0.7707 (mt-10) cc_final: 0.6946 (mp0) REVERT: A 176 MET cc_start: 0.7488 (mmp) cc_final: 0.7014 (mmt) REVERT: A 313 MET cc_start: 0.8615 (tpp) cc_final: 0.8028 (ttm) REVERT: A 325 MET cc_start: 0.8472 (mmp) cc_final: 0.8172 (mmt) REVERT: B 51 ASP cc_start: 0.7803 (m-30) cc_final: 0.7563 (t0) REVERT: B 57 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7343 (mp0) REVERT: B 81 ASP cc_start: 0.7530 (m-30) cc_final: 0.7222 (m-30) REVERT: B 87 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: C 316 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7015 (mm-30) REVERT: C 334 GLU cc_start: 0.8107 (pt0) cc_final: 0.7852 (pp20) REVERT: C 369 ILE cc_start: 0.8677 (tt) cc_final: 0.8440 (pt) REVERT: D 117 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6746 (tm-30) REVERT: D 123 MET cc_start: 0.8319 (tpp) cc_final: 0.8065 (tpt) REVERT: D 143 TYR cc_start: 0.7412 (m-80) cc_final: 0.6962 (m-80) REVERT: D 162 ASN cc_start: 0.8087 (t0) cc_final: 0.7763 (t0) REVERT: D 176 MET cc_start: 0.7386 (tpp) cc_final: 0.7076 (mtt) REVERT: D 237 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6345 (mp0) REVERT: D 283 MET cc_start: 0.8065 (mmm) cc_final: 0.7692 (mmm) REVERT: D 292 ASP cc_start: 0.8223 (t0) cc_final: 0.7946 (t0) REVERT: D 299 MET cc_start: 0.8302 (mtp) cc_final: 0.8101 (mtm) REVERT: D 313 MET cc_start: 0.8110 (ttm) cc_final: 0.7802 (ttm) REVERT: D 325 MET cc_start: 0.7578 (ttm) cc_final: 0.7311 (ttm) REVERT: E 57 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7758 (mp0) REVERT: E 68 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7914 (mmtt) REVERT: E 96 VAL cc_start: 0.8251 (p) cc_final: 0.7964 (m) REVERT: E 224 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7516 (tm-30) REVERT: E 283 MET cc_start: 0.7183 (mmp) cc_final: 0.6935 (mmm) REVERT: E 303 THR cc_start: 0.8786 (p) cc_final: 0.8493 (t) REVERT: E 316 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7555 (mm-30) outliers start: 37 outliers final: 32 residues processed: 255 average time/residue: 0.1036 time to fit residues: 41.5461 Evaluate side-chains 253 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 92 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS B 12 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.101623 restraints weight = 21384.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104859 restraints weight = 11859.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107083 restraints weight = 7385.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108619 restraints weight = 4996.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109691 restraints weight = 3590.118| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14915 Z= 0.114 Angle : 0.607 9.042 20270 Z= 0.289 Chirality : 0.047 0.335 2260 Planarity : 0.004 0.039 2565 Dihedral : 8.325 118.114 2065 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.21 % Allowed : 18.31 % Favored : 79.48 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1775 helix: 1.69 (0.19), residues: 750 sheet: -0.01 (0.27), residues: 345 loop : 1.12 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.009 0.001 TYR E 306 PHE 0.015 0.001 PHE D 352 TRP 0.013 0.001 TRP D 340 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (14905) covalent geometry : angle 0.60547 / 0.29 (20240) hydrogen bonds : bond 0.02894 / 1.98 ( 790) hydrogen bonds : angle 4.67866 / 3.35 ( 1995) link_TRANS : bond 0.00267 / 0.17 ( 10) link_TRANS : angle 1.34160 / 0.74 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 113 LYS cc_start: 0.7923 (mttm) cc_final: 0.6335 (mptt) REVERT: A 117 GLU cc_start: 0.7708 (mt-10) cc_final: 0.6976 (mp0) REVERT: A 176 MET cc_start: 0.7461 (mmp) cc_final: 0.7013 (mmt) REVERT: A 313 MET cc_start: 0.8535 (tpp) cc_final: 0.7949 (ttm) REVERT: A 325 MET cc_start: 0.8406 (mmp) cc_final: 0.8174 (mpp) REVERT: B 51 ASP cc_start: 0.7789 (m-30) cc_final: 0.7571 (t0) REVERT: B 57 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7326 (mp0) REVERT: B 81 ASP cc_start: 0.7371 (m-30) cc_final: 0.7089 (m-30) REVERT: B 87 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.7015 (t-90) REVERT: C 12 ASN cc_start: 0.8753 (m-40) cc_final: 0.8398 (t0) REVERT: C 121 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7045 (tt0) REVERT: C 292 ASP cc_start: 0.7400 (m-30) cc_final: 0.7120 (m-30) REVERT: C 316 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6990 (mm-30) REVERT: C 334 GLU cc_start: 0.8078 (pt0) cc_final: 0.7866 (pp20) REVERT: C 369 ILE cc_start: 0.8538 (tt) cc_final: 0.8249 (pt) REVERT: D 117 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6635 (tm-30) REVERT: D 123 MET cc_start: 0.8306 (tpp) cc_final: 0.8057 (tpt) REVERT: D 143 TYR cc_start: 0.7348 (m-80) cc_final: 0.6949 (m-80) REVERT: D 162 ASN cc_start: 0.8023 (t0) cc_final: 0.7621 (t0) REVERT: D 176 MET cc_start: 0.7333 (tpp) cc_final: 0.7059 (mtt) REVERT: D 237 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: D 271 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.8139 (p) REVERT: D 283 MET cc_start: 0.8124 (mmm) cc_final: 0.7782 (mmm) REVERT: D 292 ASP cc_start: 0.8135 (t0) cc_final: 0.7794 (t0) REVERT: D 299 MET cc_start: 0.8283 (mtp) cc_final: 0.7782 (mtp) REVERT: D 305 MET cc_start: 0.7153 (mmm) cc_final: 0.6890 (tmm) REVERT: D 313 MET cc_start: 0.7944 (ttm) cc_final: 0.7664 (ttm) REVERT: E 57 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7745 (mp0) REVERT: E 96 VAL cc_start: 0.8241 (p) cc_final: 0.7961 (m) REVERT: E 224 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 271 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8096 (p) REVERT: E 283 MET cc_start: 0.7123 (mmp) cc_final: 0.6894 (mmm) REVERT: E 303 THR cc_start: 0.8774 (p) cc_final: 0.8507 (t) REVERT: E 316 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7519 (mm-30) outliers start: 34 outliers final: 24 residues processed: 267 average time/residue: 0.0969 time to fit residues: 41.3924 Evaluate side-chains 251 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 87 HIS Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 148 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 121 GLN D 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106346 restraints weight = 20926.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.109157 restraints weight = 12171.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111070 restraints weight = 7840.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.112396 restraints weight = 5418.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.113341 restraints weight = 3968.280| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14915 Z= 0.120 Angle : 0.613 9.221 20270 Z= 0.293 Chirality : 0.047 0.344 2260 Planarity : 0.004 0.037 2565 Dihedral : 8.135 118.409 2065 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.14 % Allowed : 18.57 % Favored : 79.29 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1775 helix: 1.69 (0.19), residues: 755 sheet: -0.01 (0.27), residues: 345 loop : 1.13 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.008 0.001 TYR E 69 PHE 0.014 0.001 PHE D 352 TRP 0.010 0.001 TRP D 340 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14905) covalent geometry : angle 0.61152 / 0.29 (20240) hydrogen bonds : bond 0.02937 / 2.00 ( 790) hydrogen bonds : angle 4.64660 / 3.32 ( 1995) link_TRANS : bond 0.00271 / 0.17 ( 10) link_TRANS : angle 1.35107 / 0.74 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.64 seconds wall clock time: 40 minutes 25.29 seconds (2425.29 seconds total)