Starting phenix.real_space_refine on Thu Sep 18 07:01:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t25_10367/09_2025/6t25_10367.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t25_10367/09_2025/6t25_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_2025/6t25_10367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2025/6t25_10367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2025/6t25_10367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t25_10367/09_2025/6t25_10367.map" } 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-2.0-5805/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 2.68, per 1000 atoms: 0.18 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: 1.40 Conformation dependent library (CDL) restraints added in 664.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.75 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: 2.64 Time building geometry restraints manager: 1.64 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: 8830 30.11 - 60.21: 115 60.21 - 90.32: 30 90.32 - 120.42: 0 120.42 - 150.53: 10 Dihedral angle restraints: 8985 sinusoidal: 3650 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 8982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 815 0.048 - 0.097: 761 0.097 - 0.145: 478 0.145 - 0.194: 161 0.194 - 0.242: 45 Chirality restraints: 2260 Sorted by residual: chirality pdb=" CA LYS D 113 " pdb=" N LYS D 113 " pdb=" C LYS D 113 " pdb=" CB LYS D 113 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LYS E 113 " pdb=" N LYS E 113 " pdb=" C LYS E 113 " pdb=" CB LYS E 113 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS B 113 " pdb=" N LYS B 113 " pdb=" C LYS B 113 " pdb=" CB LYS B 113 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (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: 0.04 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: 1.010 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.089 0.242 2260 Planarity : 0.006 0.046 2565 Dihedral : 12.253 150.531 5535 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 aren 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 covalent geometry : bond 0.01829 (14905) covalent geometry : angle 1.59072 (20240) hydrogen bonds : bond 0.18642 ( 790) hydrogen bonds : angle 7.65629 ( 1995) link_TRANS : bond 0.00767 ( 10) link_TRANS : angle 4.11582 ( 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 : 0.532 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: 0.5973 (ttp-170) REVERT: B 34 ILE cc_start: 0.8755 (mt) cc_final: 0.8515 (pt) REVERT: B 59 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6825 (mm-40) REVERT: B 151 ILE cc_start: 0.8592 (mt) cc_final: 0.8258 (tt) REVERT: B 202 THR cc_start: 0.7519 (p) cc_final: 0.6810 (p) REVERT: B 325 MET cc_start: 0.7814 (mmm) cc_final: 0.7463 (mmt) REVERT: C 143 TYR cc_start: 0.8430 (m-80) cc_final: 0.8120 (m-10) REVERT: C 227 MET cc_start: 0.8113 (mmm) cc_final: 0.7740 (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: 0.7331 (tm-30) REVERT: D 202 THR cc_start: 0.7912 (p) cc_final: 0.7098 (p) REVERT: D 222 ASP cc_start: 0.8283 (t0) cc_final: 0.7517 (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: 0.8906 (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: 0.6381 (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: 0.1238 time to fit residues: 93.7489 Evaluate side-chains 234 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 0.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 115 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 = 0.125529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113724 restraints weight = 20236.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116760 restraints weight = 11592.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118814 restraints weight = 7390.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120244 restraints weight = 5056.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121191 restraints weight = 3659.783| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14915 Z= 0.148 Angle : 0.677 7.268 20270 Z= 0.335 Chirality : 0.047 0.234 2260 Planarity : 0.004 0.029 2565 Dihedral : 11.745 149.421 2116 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.95 % Allowed : 9.35 % Favored : 88.70 % 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 aren not related in a simple way. whole: 0.98 (0.20), residues: 1775 helix: 0.87 (0.18), residues: 785 sheet: -0.34 (0.27), residues: 315 loop : 1.21 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 256 TYR 0.017 0.001 TYR A 166 PHE 0.011 0.001 PHE A 124 TRP 0.016 0.002 TRP I 1 HIS 0.008 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00330 (14905) covalent geometry : angle 0.67669 (20240) hydrogen bonds : bond 0.04167 ( 790) hydrogen bonds : angle 5.36445 ( 1995) link_TRANS : bond 0.00094 ( 10) link_TRANS : angle 0.53700 ( 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 362 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9259 (t) cc_final: 0.8793 (m) REVERT: A 113 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.6339 (mmtt) REVERT: A 176 MET cc_start: 0.7177 (mmp) cc_final: 0.6571 (mmt) REVERT: A 279 TYR cc_start: 0.8640 (t80) cc_final: 0.8418 (t80) REVERT: A 313 MET cc_start: 0.8048 (tpp) cc_final: 0.7773 (ttm) REVERT: A 325 MET cc_start: 0.7125 (mmp) cc_final: 0.6743 (tpp) REVERT: B 83 GLU cc_start: 0.7688 (tt0) cc_final: 0.7177 (tm-30) REVERT: B 88 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6354 (t-90) REVERT: B 210 ARG cc_start: 0.7345 (ttp80) cc_final: 0.7030 (ttm170) REVERT: B 244 ASP cc_start: 0.7641 (p0) cc_final: 0.7432 (p0) REVERT: C 57 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7039 (mt-10) REVERT: C 162 ASN cc_start: 0.8185 (t0) cc_final: 0.7932 (t0) REVERT: D 117 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6957 (tm-30) REVERT: D 143 TYR cc_start: 0.7429 (m-80) cc_final: 0.6759 (m-80) REVERT: D 162 ASN cc_start: 0.7872 (t0) cc_final: 0.7601 (t0) REVERT: D 176 MET cc_start: 0.7108 (mmp) cc_final: 0.6846 (mmt) REVERT: D 283 MET cc_start: 0.7933 (mmp) cc_final: 0.7453 (mmm) REVERT: D 352 PHE cc_start: 0.8288 (t80) cc_final: 0.8033 (t80) REVERT: E 72 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7052 (mp0) REVERT: E 93 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6421 (mm-30) REVERT: E 119 MET cc_start: 0.8282 (ttm) cc_final: 0.8071 (ttm) REVERT: E 217 CYS cc_start: 0.7489 (m) cc_final: 0.6903 (m) REVERT: E 225 ASN cc_start: 0.8228 (m110) cc_final: 0.7849 (m110) REVERT: E 238 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8081 (mtpt) REVERT: E 311 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: E 325 MET cc_start: 0.6706 (mmt) cc_final: 0.6499 (tpt) outliers start: 30 outliers final: 19 residues processed: 354 average time/residue: 0.1108 time to fit residues: 59.4582 Evaluate side-chains 260 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 A residue 292 ASP 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 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 214 GLU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 123 MET 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 Chi-restraints excluded: chain G residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 8 optimal weight: 0.0060 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 297 ASN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105714 restraints weight = 21211.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109137 restraints weight = 11569.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111455 restraints weight = 7172.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113031 restraints weight = 4826.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114150 restraints weight = 3455.953| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14915 Z= 0.126 Angle : 0.621 6.723 20270 Z= 0.300 Chirality : 0.045 0.242 2260 Planarity : 0.004 0.033 2565 Dihedral : 11.137 145.388 2116 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.21 % Allowed : 12.53 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.20), residues: 1775 helix: 1.31 (0.19), residues: 785 sheet: -0.04 (0.26), residues: 345 loop : 1.49 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 95 TYR 0.015 0.001 TYR D 218 PHE 0.016 0.001 PHE C 223 TRP 0.010 0.001 TRP D 340 HIS 0.005 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00281 (14905) covalent geometry : angle 0.62157 (20240) hydrogen bonds : bond 0.03376 ( 790) hydrogen bonds : angle 4.94289 ( 1995) link_TRANS : bond 0.00169 ( 10) link_TRANS : angle 0.24560 ( 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 321 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 287 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9238 (t) cc_final: 0.8821 (m) REVERT: A 113 LYS cc_start: 0.7741 (mmtm) cc_final: 0.6286 (mmtt) REVERT: A 117 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7416 (mp0) REVERT: A 176 MET cc_start: 0.7468 (mmp) cc_final: 0.6808 (mmt) REVERT: A 279 TYR cc_start: 0.8568 (t80) cc_final: 0.8316 (t80) REVERT: A 313 MET cc_start: 0.8298 (tpp) cc_final: 0.7936 (ttm) REVERT: A 325 MET cc_start: 0.7755 (mmp) cc_final: 0.7367 (tpp) REVERT: B 83 GLU cc_start: 0.7712 (tt0) cc_final: 0.7177 (tm-30) REVERT: B 88 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6489 (t-90) REVERT: B 117 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6747 (tt0) REVERT: C 12 ASN cc_start: 0.8579 (m110) cc_final: 0.8339 (t0) REVERT: C 57 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7179 (mt-10) REVERT: C 121 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7866 (tm-30) REVERT: C 143 TYR cc_start: 0.7726 (m-80) cc_final: 0.7449 (m-10) REVERT: C 328 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8054 (ttmm) REVERT: D 117 GLU cc_start: 0.7570 (mt-10) cc_final: 0.6779 (tm-30) REVERT: D 143 TYR cc_start: 0.7380 (m-80) cc_final: 0.6943 (m-80) REVERT: D 162 ASN cc_start: 0.8000 (t0) cc_final: 0.7622 (t0) REVERT: D 283 MET cc_start: 0.8095 (mmp) cc_final: 0.7854 (mmm) REVERT: D 292 ASP cc_start: 0.8210 (t0) cc_final: 0.7685 (t0) REVERT: D 313 MET cc_start: 0.8175 (ttm) cc_final: 0.7597 (ttm) REVERT: D 334 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6523 (tp30) REVERT: E 68 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8009 (mmtt) REVERT: E 72 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7153 (mp0) REVERT: E 93 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6456 (mm-30) REVERT: E 217 CYS cc_start: 0.7526 (m) cc_final: 0.6897 (m) REVERT: E 225 ASN cc_start: 0.8362 (m110) cc_final: 0.7961 (m110) REVERT: E 311 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: E 316 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7569 (mm-30) REVERT: E 325 MET cc_start: 0.7371 (mmt) cc_final: 0.7100 (tpt) outliers start: 34 outliers final: 17 residues processed: 311 average time/residue: 0.1103 time to fit residues: 52.5750 Evaluate side-chains 248 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 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 B residue 364 GLU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain D residue 30 VAL 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 269 MET Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 311 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 160 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 88 HIS D 263 GLN E 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.100927 restraints weight = 21554.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.104124 restraints weight = 11868.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106411 restraints weight = 7463.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107964 restraints weight = 5092.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.109024 restraints weight = 3690.138| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14915 Z= 0.151 Angle : 0.649 10.920 20270 Z= 0.309 Chirality : 0.047 0.262 2260 Planarity : 0.004 0.036 2565 Dihedral : 10.777 136.428 2115 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.27 % Allowed : 14.55 % Favored : 83.18 % 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 aren not related in a simple way. whole: 1.41 (0.20), residues: 1775 helix: 1.30 (0.19), residues: 785 sheet: -0.01 (0.27), residues: 345 loop : 1.35 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 95 TYR 0.011 0.001 TYR C 198 PHE 0.027 0.001 PHE C 223 TRP 0.011 0.002 TRP D 340 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00356 (14905) covalent geometry : angle 0.64901 (20240) hydrogen bonds : bond 0.03447 ( 790) hydrogen bonds : angle 4.88910 ( 1995) link_TRANS : bond 0.00210 ( 10) link_TRANS : angle 0.42985 ( 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: 35 poor density : 271 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7072 (mp0) REVERT: A 176 MET cc_start: 0.7459 (mmp) cc_final: 0.7046 (mmt) REVERT: A 279 TYR cc_start: 0.8685 (t80) cc_final: 0.8485 (t80) REVERT: A 313 MET cc_start: 0.8431 (tpp) cc_final: 0.7956 (ttm) REVERT: A 325 MET cc_start: 0.7868 (mmp) cc_final: 0.7507 (tpp) REVERT: B 57 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7448 (mp0) REVERT: B 83 GLU cc_start: 0.7819 (tt0) cc_final: 0.7422 (tm-30) REVERT: B 88 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.6574 (t-90) REVERT: C 57 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7163 (mt-10) REVERT: C 121 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 143 TYR cc_start: 0.7628 (m-80) cc_final: 0.7379 (m-10) REVERT: C 207 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7987 (mm-30) REVERT: C 316 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7241 (mm-30) REVERT: D 88 HIS cc_start: 0.7591 (t70) cc_final: 0.7218 (t-90) REVERT: D 121 GLN cc_start: 0.8135 (tt0) cc_final: 0.7932 (tt0) REVERT: D 143 TYR cc_start: 0.7429 (m-80) cc_final: 0.7009 (m-80) REVERT: D 162 ASN cc_start: 0.8010 (t0) cc_final: 0.7655 (t0) REVERT: D 237 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: D 292 ASP cc_start: 0.8123 (t0) cc_final: 0.7660 (t70) REVERT: D 313 MET cc_start: 0.8107 (ttm) cc_final: 0.7654 (ttm) REVERT: D 325 MET cc_start: 0.7162 (mmm) cc_final: 0.6869 (ttm) REVERT: D 334 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6650 (tp30) REVERT: E 68 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7994 (mmtt) REVERT: E 217 CYS cc_start: 0.8069 (m) cc_final: 0.7502 (m) REVERT: E 316 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7410 (mm-30) REVERT: E 325 MET cc_start: 0.7520 (mmt) cc_final: 0.7173 (tpt) REVERT: E 372 ARG cc_start: 0.5819 (mtp180) cc_final: 0.5592 (mtp180) outliers start: 35 outliers final: 27 residues processed: 296 average time/residue: 0.1043 time to fit residues: 47.8495 Evaluate side-chains 253 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 320 LEU 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 323 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 358 THR 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 214 GLU Chi-restraints excluded: chain C residue 227 MET 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 248 ILE Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 314 GLN 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 178 LEU Chi-restraints excluded: chain E residue 271 SER 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: 0.3980 chunk 92 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102313 restraints weight = 21365.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105070 restraints weight = 12474.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107031 restraints weight = 8108.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.108362 restraints weight = 5638.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109309 restraints weight = 4147.981| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4978 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= 0.183 Angle : 0.661 8.655 20270 Z= 0.317 Chirality : 0.048 0.270 2260 Planarity : 0.004 0.033 2565 Dihedral : 10.453 131.833 2115 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.86 % Allowed : 15.58 % Favored : 81.56 % 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 aren not related in a simple way. whole: 1.21 (0.20), residues: 1775 helix: 1.17 (0.19), residues: 785 sheet: -0.06 (0.27), residues: 345 loop : 1.14 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 183 TYR 0.012 0.001 TYR C 198 PHE 0.021 0.002 PHE C 223 TRP 0.013 0.002 TRP D 340 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00435 (14905) covalent geometry : angle 0.66112 (20240) hydrogen bonds : bond 0.03698 ( 790) hydrogen bonds : angle 5.00208 ( 1995) link_TRANS : bond 0.00274 ( 10) link_TRANS : angle 0.50519 ( 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 283 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6849 (mp0) REVERT: A 176 MET cc_start: 0.7206 (mmp) cc_final: 0.6952 (mmt) REVERT: A 313 MET cc_start: 0.8423 (tpp) cc_final: 0.7867 (ttm) REVERT: A 325 MET cc_start: 0.8012 (mmp) cc_final: 0.7619 (mmt) REVERT: B 57 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7495 (mp0) REVERT: B 81 ASP cc_start: 0.7244 (m-30) cc_final: 0.7002 (m-30) REVERT: C 119 MET cc_start: 0.8658 (ttm) cc_final: 0.8431 (ttm) REVERT: C 121 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 143 TYR cc_start: 0.7661 (m-80) cc_final: 0.7430 (m-10) REVERT: C 227 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.6895 (mpp) REVERT: C 316 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7018 (mm-30) REVERT: C 334 GLU cc_start: 0.8010 (pt0) cc_final: 0.7761 (pp20) REVERT: D 88 HIS cc_start: 0.7589 (t70) cc_final: 0.7328 (t-90) REVERT: D 121 GLN cc_start: 0.8105 (tt0) cc_final: 0.7897 (tt0) REVERT: D 123 MET cc_start: 0.8175 (tpp) cc_final: 0.7839 (tpt) REVERT: D 143 TYR cc_start: 0.7436 (m-80) cc_final: 0.7004 (m-80) REVERT: D 162 ASN cc_start: 0.8033 (t0) cc_final: 0.7720 (t0) REVERT: D 334 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6710 (tp30) REVERT: E 57 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7475 (mp0) REVERT: E 68 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7947 (mmtt) REVERT: E 226 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8155 (mm-30) REVERT: E 283 MET cc_start: 0.7110 (mmp) cc_final: 0.6756 (mmm) REVERT: E 325 MET cc_start: 0.7488 (mmt) cc_final: 0.7072 (tpt) outliers start: 44 outliers final: 36 residues processed: 271 average time/residue: 0.1021 time to fit residues: 43.4184 Evaluate side-chains 262 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 224 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 194 THR 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 88 HIS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 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 34 ILE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 227 MET 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 248 ILE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 305 MET 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 178 LEU Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 146 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.098357 restraints weight = 21609.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101564 restraints weight = 11959.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103773 restraints weight = 7490.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105263 restraints weight = 5068.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106340 restraints weight = 3681.171| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14915 Z= 0.156 Angle : 0.637 9.158 20270 Z= 0.303 Chirality : 0.047 0.267 2260 Planarity : 0.004 0.034 2565 Dihedral : 9.998 126.155 2115 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.92 % Allowed : 16.10 % Favored : 80.97 % 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 aren not related in a simple way. whole: 1.35 (0.20), residues: 1775 helix: 1.44 (0.19), residues: 755 sheet: -0.10 (0.27), residues: 345 loop : 1.08 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.010 0.001 TYR C 198 PHE 0.019 0.001 PHE D 352 TRP 0.014 0.002 TRP D 340 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00368 (14905) covalent geometry : angle 0.63754 (20240) hydrogen bonds : bond 0.03372 ( 790) hydrogen bonds : angle 4.91641 ( 1995) link_TRANS : bond 0.00235 ( 10) link_TRANS : angle 0.44283 ( 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 281 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6780 (mp0) REVERT: A 176 MET cc_start: 0.7434 (mmp) cc_final: 0.7025 (mmt) REVERT: A 192 ILE cc_start: 0.8658 (mm) cc_final: 0.8090 (tt) REVERT: A 313 MET cc_start: 0.8482 (tpp) cc_final: 0.7861 (ttm) REVERT: A 325 MET cc_start: 0.8433 (mmp) cc_final: 0.8106 (mmt) REVERT: B 57 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7513 (mp0) REVERT: B 81 ASP cc_start: 0.7513 (m-30) cc_final: 0.7176 (m-30) REVERT: B 117 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7233 (tm-30) REVERT: C 115 ASN cc_start: 0.8988 (OUTLIER) cc_final: 0.8501 (t0) REVERT: C 121 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 143 TYR cc_start: 0.7579 (m-80) cc_final: 0.7342 (m-10) REVERT: C 227 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.6804 (mpp) REVERT: C 316 GLU cc_start: 0.7835 (mm-30) cc_final: 0.6990 (mm-30) REVERT: C 334 GLU cc_start: 0.8123 (pt0) cc_final: 0.7783 (pp20) REVERT: D 88 HIS cc_start: 0.7640 (t70) cc_final: 0.7405 (t70) REVERT: D 100 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6472 (mp0) REVERT: D 121 GLN cc_start: 0.8166 (tt0) cc_final: 0.7917 (tt0) REVERT: D 123 MET cc_start: 0.8350 (tpp) cc_final: 0.8039 (tpt) REVERT: D 143 TYR cc_start: 0.7397 (m-80) cc_final: 0.6985 (m-80) REVERT: D 162 ASN cc_start: 0.8033 (t0) cc_final: 0.7655 (t0) REVERT: D 237 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: D 283 MET cc_start: 0.8146 (mmm) cc_final: 0.7704 (mmm) REVERT: D 313 MET cc_start: 0.8062 (ttm) cc_final: 0.7620 (ttm) REVERT: D 316 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7089 (mp0) REVERT: D 334 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: E 57 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7712 (mp0) REVERT: E 68 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7852 (mmtt) REVERT: E 244 ASP cc_start: 0.7368 (p0) cc_final: 0.7052 (t0) REVERT: E 283 MET cc_start: 0.7088 (mmp) cc_final: 0.6795 (mmm) REVERT: E 303 THR cc_start: 0.8872 (p) cc_final: 0.8530 (t) REVERT: E 325 MET cc_start: 0.7770 (mmt) cc_final: 0.7372 (tpt) outliers start: 45 outliers final: 34 residues processed: 269 average time/residue: 0.0996 time to fit residues: 42.0822 Evaluate side-chains 265 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 194 THR 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 88 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 348 SER 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 115 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 227 MET 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 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 D residue 305 MET 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 178 LEU Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 20 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 137 GLN ** 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 = 0.3262 r_free = 0.3262 target = 0.112983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100232 restraints weight = 21441.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.103493 restraints weight = 11823.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.105695 restraints weight = 7361.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.107210 restraints weight = 4966.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108193 restraints weight = 3582.928| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5343 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= 0.126 Angle : 0.608 7.493 20270 Z= 0.287 Chirality : 0.046 0.256 2260 Planarity : 0.004 0.036 2565 Dihedral : 9.405 117.954 2115 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.66 % Allowed : 16.43 % Favored : 80.91 % 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 aren not related in a simple way. whole: 1.44 (0.20), residues: 1775 helix: 1.51 (0.19), residues: 755 sheet: -0.05 (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 0.010 0.001 TYR D 69 PHE 0.020 0.001 PHE D 352 TRP 0.014 0.001 TRP D 340 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00289 (14905) covalent geometry : angle 0.60796 (20240) hydrogen bonds : bond 0.03074 ( 790) hydrogen bonds : angle 4.80483 ( 1995) link_TRANS : bond 0.00175 ( 10) link_TRANS : angle 0.37940 ( 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 287 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6742 (mp0) REVERT: A 176 MET cc_start: 0.7464 (mmp) cc_final: 0.7065 (mmt) REVERT: A 303 THR cc_start: 0.8768 (p) cc_final: 0.8489 (t) REVERT: A 313 MET cc_start: 0.8525 (tpp) cc_final: 0.7946 (ttm) REVERT: A 325 MET cc_start: 0.8486 (mmp) cc_final: 0.8144 (mmt) REVERT: B 51 ASP cc_start: 0.7874 (m-30) cc_final: 0.7473 (t0) REVERT: B 81 ASP cc_start: 0.7454 (m-30) cc_final: 0.7130 (m-30) REVERT: B 117 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7119 (tm-30) REVERT: C 49 GLN cc_start: 0.6754 (mt0) cc_final: 0.6509 (mt0) REVERT: C 121 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8074 (tm-30) REVERT: C 123 MET cc_start: 0.8189 (tpp) cc_final: 0.7592 (tpp) REVERT: C 316 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6962 (mm-30) REVERT: C 334 GLU cc_start: 0.8088 (pt0) cc_final: 0.7774 (pp20) REVERT: C 369 ILE cc_start: 0.8713 (tt) cc_final: 0.8479 (pt) REVERT: D 100 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6604 (mp0) REVERT: D 121 GLN cc_start: 0.8050 (tt0) cc_final: 0.7827 (tt0) REVERT: D 123 MET cc_start: 0.8380 (tpp) cc_final: 0.8044 (tpt) REVERT: D 143 TYR cc_start: 0.7357 (m-80) cc_final: 0.6944 (m-80) REVERT: D 162 ASN cc_start: 0.8181 (t0) cc_final: 0.7760 (t0) REVERT: D 283 MET cc_start: 0.8200 (mmm) cc_final: 0.7749 (mmm) REVERT: D 313 MET cc_start: 0.8025 (ttm) cc_final: 0.7680 (ttm) REVERT: E 57 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7715 (mp0) REVERT: E 68 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7861 (mmtt) REVERT: E 96 VAL cc_start: 0.8358 (p) cc_final: 0.8067 (m) REVERT: E 244 ASP cc_start: 0.7732 (p0) cc_final: 0.7451 (t0) REVERT: E 283 MET cc_start: 0.7102 (mmp) cc_final: 0.6846 (mmm) REVERT: E 303 THR cc_start: 0.8891 (p) cc_final: 0.8571 (t) outliers start: 41 outliers final: 34 residues processed: 273 average time/residue: 0.1069 time to fit residues: 45.9501 Evaluate side-chains 264 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 230 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 323 SER 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 6 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 ILE 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 216 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 305 MET 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 178 LEU Chi-restraints excluded: chain E residue 271 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 81 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 0.0470 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102568 restraints weight = 21382.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105868 restraints weight = 11695.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108091 restraints weight = 7233.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.109610 restraints weight = 4877.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.110702 restraints weight = 3486.819| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14915 Z= 0.109 Angle : 0.602 8.869 20270 Z= 0.283 Chirality : 0.046 0.252 2260 Planarity : 0.004 0.036 2565 Dihedral : 8.719 118.048 2115 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.08 % Allowed : 17.60 % Favored : 80.32 % 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 aren not related in a simple way. whole: 1.57 (0.20), residues: 1775 helix: 1.63 (0.19), residues: 755 sheet: 0.02 (0.27), residues: 345 loop : 1.17 (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 306 PHE 0.020 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 covalent geometry : bond 0.00244 (14905) covalent geometry : angle 0.60189 (20240) hydrogen bonds : bond 0.02863 ( 790) hydrogen bonds : angle 4.68511 ( 1995) link_TRANS : bond 0.00127 ( 10) link_TRANS : angle 0.33823 ( 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 295 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 0.569 Fit side-chains REVERT: A 113 LYS cc_start: 0.7818 (mttm) cc_final: 0.6382 (mptt) REVERT: A 117 GLU cc_start: 0.7508 (mt-10) cc_final: 0.6670 (mp0) REVERT: A 176 MET cc_start: 0.7494 (mmp) cc_final: 0.7033 (mmt) REVERT: A 227 MET cc_start: 0.8027 (mmm) cc_final: 0.7763 (mmm) REVERT: A 283 MET cc_start: 0.7605 (mmm) cc_final: 0.7404 (mmm) REVERT: A 303 THR cc_start: 0.8724 (p) cc_final: 0.8515 (t) REVERT: A 313 MET cc_start: 0.8512 (tpp) cc_final: 0.7958 (ttm) REVERT: A 325 MET cc_start: 0.8456 (mmp) cc_final: 0.8147 (mmt) REVERT: B 51 ASP cc_start: 0.7862 (m-30) cc_final: 0.7518 (t0) REVERT: B 81 ASP cc_start: 0.7380 (m-30) cc_final: 0.7082 (m-30) REVERT: C 49 GLN cc_start: 0.6720 (mt0) cc_final: 0.6436 (mt0) REVERT: C 123 MET cc_start: 0.8195 (tpp) cc_final: 0.7586 (tpp) REVERT: C 316 GLU cc_start: 0.7730 (mm-30) cc_final: 0.6980 (mm-30) REVERT: C 334 GLU cc_start: 0.8048 (pt0) cc_final: 0.7765 (pp20) REVERT: D 117 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6630 (tm-30) REVERT: D 123 MET cc_start: 0.8447 (tpp) cc_final: 0.8099 (tpt) REVERT: D 143 TYR cc_start: 0.7321 (m-80) cc_final: 0.6936 (m-80) REVERT: D 162 ASN cc_start: 0.8127 (t0) cc_final: 0.7652 (t0) REVERT: D 237 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: D 283 MET cc_start: 0.8192 (mmm) cc_final: 0.7702 (mmm) REVERT: D 313 MET cc_start: 0.7939 (ttm) cc_final: 0.7625 (ttm) REVERT: E 57 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7736 (mp0) REVERT: E 68 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7981 (mmtt) REVERT: E 96 VAL cc_start: 0.8222 (p) cc_final: 0.7918 (m) REVERT: E 283 MET cc_start: 0.6986 (mmp) cc_final: 0.6769 (mmm) REVERT: E 303 THR cc_start: 0.8757 (p) cc_final: 0.8502 (t) outliers start: 32 outliers final: 30 residues processed: 285 average time/residue: 0.1038 time to fit residues: 46.7024 Evaluate side-chains 261 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 320 LEU 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 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 323 SER 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 6 THR 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 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 305 MET 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 178 LEU 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: 1.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 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 ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103563 restraints weight = 21078.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106448 restraints weight = 12118.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108417 restraints weight = 7743.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109776 restraints weight = 5347.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110713 restraints weight = 3900.971| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14915 Z= 0.227 Angle : 0.709 10.503 20270 Z= 0.343 Chirality : 0.049 0.283 2260 Planarity : 0.005 0.041 2565 Dihedral : 9.146 117.249 2115 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.79 % Allowed : 18.05 % Favored : 79.16 % 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 aren not related in a simple way. whole: 1.12 (0.20), residues: 1775 helix: 1.26 (0.19), residues: 755 sheet: -0.16 (0.27), residues: 345 loop : 0.91 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 183 TYR 0.014 0.002 TYR C 198 PHE 0.022 0.002 PHE D 352 TRP 0.012 0.002 TRP B 340 HIS 0.009 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00542 (14905) covalent geometry : angle 0.70897 (20240) hydrogen bonds : bond 0.03961 ( 790) hydrogen bonds : angle 5.02431 ( 1995) link_TRANS : bond 0.00328 ( 10) link_TRANS : angle 0.70976 ( 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 266 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.578 Fit side-chains REVERT: A 113 LYS cc_start: 0.8076 (mttm) cc_final: 0.6591 (mptt) REVERT: A 117 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6938 (mp0) REVERT: A 176 MET cc_start: 0.7256 (mmp) cc_final: 0.6907 (mmt) REVERT: A 192 ILE cc_start: 0.8826 (mm) cc_final: 0.8354 (tt) REVERT: A 283 MET cc_start: 0.7750 (mmm) cc_final: 0.7304 (mmm) REVERT: A 313 MET cc_start: 0.8550 (tpp) cc_final: 0.8136 (tpp) REVERT: A 325 MET cc_start: 0.8281 (mmp) cc_final: 0.7954 (mmt) REVERT: B 81 ASP cc_start: 0.7486 (m-30) cc_final: 0.7192 (m-30) REVERT: B 87 HIS cc_start: 0.7495 (OUTLIER) cc_final: 0.7037 (t-90) REVERT: C 316 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7241 (mm-30) REVERT: C 334 GLU cc_start: 0.8027 (pt0) cc_final: 0.7795 (pp20) REVERT: D 123 MET cc_start: 0.8264 (tpp) cc_final: 0.7976 (tpt) REVERT: D 143 TYR cc_start: 0.7469 (m-80) cc_final: 0.7024 (m-80) REVERT: D 237 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: D 288 ASP cc_start: 0.7343 (t0) cc_final: 0.7130 (t70) REVERT: D 334 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 57 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7669 (mp0) REVERT: E 96 VAL cc_start: 0.8305 (p) cc_final: 0.8033 (m) REVERT: E 283 MET cc_start: 0.7177 (mmp) cc_final: 0.6973 (mmm) REVERT: E 303 THR cc_start: 0.8799 (p) cc_final: 0.8489 (t) outliers start: 43 outliers final: 36 residues processed: 256 average time/residue: 0.1105 time to fit residues: 43.9028 Evaluate side-chains 250 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 194 THR 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 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 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 30 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 71 ILE 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 216 LEU 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 305 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 178 LEU 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: 0.9980 chunk 14 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099458 restraints weight = 21501.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.102671 restraints weight = 11897.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.104833 restraints weight = 7424.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106350 restraints weight = 5023.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.107344 restraints weight = 3619.731| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14915 Z= 0.139 Angle : 0.637 7.966 20270 Z= 0.305 Chirality : 0.047 0.267 2260 Planarity : 0.004 0.044 2565 Dihedral : 8.681 119.831 2115 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.34 % Allowed : 18.44 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.20), residues: 1775 helix: 1.40 (0.19), residues: 755 sheet: -0.08 (0.27), residues: 345 loop : 0.97 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.010 0.001 TYR D 69 PHE 0.021 0.001 PHE D 352 TRP 0.013 0.001 TRP D 340 HIS 0.008 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00326 (14905) covalent geometry : angle 0.63756 (20240) hydrogen bonds : bond 0.03202 ( 790) hydrogen bonds : angle 4.85532 ( 1995) link_TRANS : bond 0.00196 ( 10) link_TRANS : angle 0.42280 ( 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 270 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.587 Fit side-chains REVERT: A 113 LYS cc_start: 0.8022 (mttm) cc_final: 0.6500 (mptt) REVERT: A 117 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6742 (mp0) REVERT: A 176 MET cc_start: 0.7433 (mmp) cc_final: 0.7001 (mmt) REVERT: A 283 MET cc_start: 0.7667 (mmm) cc_final: 0.7246 (mmm) REVERT: A 313 MET cc_start: 0.8563 (tpp) cc_final: 0.7981 (ttm) REVERT: A 325 MET cc_start: 0.8377 (mmp) cc_final: 0.8024 (mmt) REVERT: B 81 ASP cc_start: 0.7454 (m-30) cc_final: 0.7111 (m-30) REVERT: B 87 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6756 (t-90) REVERT: C 12 ASN cc_start: 0.8777 (m-40) cc_final: 0.8373 (t0) REVERT: C 123 MET cc_start: 0.8272 (tpp) cc_final: 0.7521 (tpp) REVERT: C 316 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7029 (mm-30) REVERT: C 334 GLU cc_start: 0.8102 (pt0) cc_final: 0.7836 (pp20) REVERT: D 123 MET cc_start: 0.8358 (tpp) cc_final: 0.8022 (tpt) REVERT: D 143 TYR cc_start: 0.7400 (m-80) cc_final: 0.7002 (m-80) REVERT: D 237 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: D 288 ASP cc_start: 0.7563 (t0) cc_final: 0.7287 (t70) REVERT: D 334 GLU cc_start: 0.7307 (tm-30) cc_final: 0.7038 (tm-30) REVERT: E 57 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7729 (mp0) REVERT: E 68 LYS cc_start: 0.8076 (mmtt) cc_final: 0.7873 (mmtt) REVERT: E 96 VAL cc_start: 0.8218 (p) cc_final: 0.7921 (m) REVERT: E 123 MET cc_start: 0.7948 (tpp) cc_final: 0.7375 (tpt) REVERT: E 283 MET cc_start: 0.7118 (mmp) cc_final: 0.6900 (mmm) REVERT: E 303 THR cc_start: 0.8853 (p) cc_final: 0.8561 (t) outliers start: 36 outliers final: 33 residues processed: 259 average time/residue: 0.1030 time to fit residues: 42.2840 Evaluate side-chains 258 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP 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 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 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 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 269 MET Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 178 LEU 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: 6.9990 chunk 156 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101225 restraints weight = 21390.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.104421 restraints weight = 11816.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.106602 restraints weight = 7403.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108101 restraints weight = 5008.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109159 restraints weight = 3606.073| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14915 Z= 0.126 Angle : 0.624 7.665 20270 Z= 0.296 Chirality : 0.046 0.261 2260 Planarity : 0.004 0.041 2565 Dihedral : 8.380 123.412 2115 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.40 % Allowed : 18.83 % Favored : 78.77 % 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 aren not related in a simple way. whole: 1.37 (0.20), residues: 1775 helix: 1.49 (0.19), residues: 755 sheet: -0.04 (0.27), residues: 345 loop : 1.02 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.009 0.001 TYR D 69 PHE 0.022 0.001 PHE D 352 TRP 0.013 0.001 TRP D 340 HIS 0.005 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00291 (14905) covalent geometry : angle 0.62414 (20240) hydrogen bonds : bond 0.03054 ( 790) hydrogen bonds : angle 4.75827 ( 1995) link_TRANS : bond 0.00166 ( 10) link_TRANS : angle 0.42297 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2215.39 seconds wall clock time: 39 minutes 21.76 seconds (2361.76 seconds total)