Starting phenix.real_space_refine on Wed Mar 4 12:24:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k25_22643/03_2026/7k25_22643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k25_22643/03_2026/7k25_22643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k25_22643/03_2026/7k25_22643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k25_22643/03_2026/7k25_22643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k25_22643/03_2026/7k25_22643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k25_22643/03_2026/7k25_22643.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 8863 2.51 5 N 2352 2.21 5 O 2711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14005 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2854 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 31, 'TRANS': 334} Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 31, 'TRANS': 335} Chain: "C" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2789 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 30, 'TRANS': 326} Chain: "D" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2650 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 27, 'TRANS': 312} Chain: "E" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2850 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 334} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.47, per 1000 atoms: 0.25 Number of scatterers: 14005 At special positions: 0 Unit cell: (167.2, 163.9, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 79 16.00 O 2711 8.00 N 2352 7.00 C 8863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS E 3 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS C 98 " distance=2.04 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS E 98 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 624.5 milliseconds 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 32 sheets defined 11.5% alpha, 38.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.524A pdb=" N LEU B 23 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 79 removed outlier: 3.630A pdb=" N LEU B 79 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 304 through 315 removed outlier: 3.514A pdb=" N LEU B 308 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 115 through 121 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.954A pdb=" N LEU C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 357 Processing helix chain 'D' and resid 17 through 23 Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 115 through 121 Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.547A pdb=" N ILE D 180 " --> pdb=" O THR D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 304 through 317 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 75 through 79 Processing helix chain 'E' and resid 116 through 121 Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 186 through 191 Processing helix chain 'E' and resid 304 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.458A pdb=" N TYR A 289 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 111 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 291 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 109 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 293 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.458A pdb=" N TYR A 289 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 111 " --> pdb=" O TYR A 289 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A 291 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 109 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR A 293 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TRP A 104 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 88 removed outlier: 6.465A pdb=" N ARG A 284 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TRP A 272 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS A 282 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.203A pdb=" N ILE A 137 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AA7, first strand: chain 'A' and resid 236 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.585A pdb=" N ARG B 284 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP B 272 " --> pdb=" O HIS B 282 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS B 282 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AB1, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.491A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 37 removed outlier: 6.491A pdb=" N TYR B 289 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 111 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS B 291 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 109 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 293 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.309A pdb=" N ILE B 137 " --> pdb=" O PRO B 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 197 through 198 Processing sheet with id=AB5, first strand: chain 'B' and resid 236 through 240 Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 240 removed outlier: 4.056A pdb=" N GLY C 271 " --> pdb=" O ARG C 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 352 through 355 removed outlier: 4.029A pdb=" N GLY B 358 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.509A pdb=" N TYR C 289 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR C 111 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS C 291 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C 109 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C 293 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 31 through 37 removed outlier: 6.509A pdb=" N TYR C 289 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR C 111 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS C 291 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL C 109 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR C 293 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP C 104 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.229A pdb=" N ILE C 137 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 197 through 199 Processing sheet with id=AC3, first strand: chain 'C' and resid 236 through 240 Processing sheet with id=AC4, first strand: chain 'C' and resid 236 through 240 removed outlier: 6.677A pdb=" N ARG D 284 " --> pdb=" O MET D 270 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 31 through 37 removed outlier: 6.520A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 31 through 37 removed outlier: 6.520A pdb=" N TYR D 289 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR D 111 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS D 291 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D 109 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 293 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 128 through 130 removed outlier: 6.482A pdb=" N ILE D 137 " --> pdb=" O PRO D 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 197 through 200 removed outlier: 4.192A pdb=" N LEU D 156 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 236 through 240 Processing sheet with id=AD1, first strand: chain 'D' and resid 236 through 240 removed outlier: 6.697A pdb=" N ARG E 284 " --> pdb=" O MET E 270 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP E 272 " --> pdb=" O HIS E 282 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N HIS E 282 " --> pdb=" O TRP E 272 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 31 through 37 removed outlier: 3.729A pdb=" N SER E 108 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG E 295 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA E 106 " --> pdb=" O ARG E 295 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG E 297 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TRP E 104 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 299 " --> pdb=" O GLN E 102 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN E 102 " --> pdb=" O VAL E 299 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 128 through 130 removed outlier: 6.185A pdb=" N ILE E 137 " --> pdb=" O PRO E 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 197 through 199 Processing sheet with id=AD5, first strand: chain 'E' and resid 351 through 354 removed outlier: 3.934A pdb=" N THR E 351 " --> pdb=" O THR E 362 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 353 " --> pdb=" O THR E 360 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1224 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: 2.50 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2398 1.30 - 1.43: 3570 1.43 - 1.57: 8245 1.57 - 1.70: 0 1.70 - 1.83: 138 Bond restraints: 14351 Sorted by residual: bond pdb=" C GLY D 322 " pdb=" O GLY D 322 " ideal model delta sigma weight residual 1.232 1.169 0.064 1.43e-02 4.89e+03 1.98e+01 bond pdb=" N LEU E 96 " pdb=" CA LEU E 96 " ideal model delta sigma weight residual 1.457 1.512 -0.054 1.29e-02 6.01e+03 1.76e+01 bond pdb=" CA THR E 97 " pdb=" C THR E 97 " ideal model delta sigma weight residual 1.521 1.557 -0.036 1.28e-02 6.10e+03 8.05e+00 bond pdb=" C PRO B 213 " pdb=" N ASP B 214 " ideal model delta sigma weight residual 1.331 1.295 0.037 1.63e-02 3.76e+03 5.06e+00 bond pdb=" N THR E 97 " pdb=" CA THR E 97 " ideal model delta sigma weight residual 1.455 1.483 -0.027 1.23e-02 6.61e+03 4.92e+00 ... (remaining 14346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 18725 2.05 - 4.10: 726 4.10 - 6.14: 90 6.14 - 8.19: 18 8.19 - 10.24: 10 Bond angle restraints: 19569 Sorted by residual: angle pdb=" C THR E 100 " pdb=" N LEU E 101 " pdb=" CA LEU E 101 " ideal model delta sigma weight residual 122.15 132.39 -10.24 1.74e+00 3.30e-01 3.46e+01 angle pdb=" N GLY D 322 " pdb=" CA GLY D 322 " pdb=" C GLY D 322 " ideal model delta sigma weight residual 112.61 121.47 -8.86 1.60e+00 3.91e-01 3.07e+01 angle pdb=" C PRO C 213 " pdb=" N ASP C 214 " pdb=" CA ASP C 214 " ideal model delta sigma weight residual 121.20 128.16 -6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" C CYS E 3 " pdb=" N PRO E 4 " pdb=" CA PRO E 4 " ideal model delta sigma weight residual 119.76 124.66 -4.90 1.03e+00 9.43e-01 2.26e+01 angle pdb=" CA GLY D 54 " pdb=" C GLY D 54 " pdb=" N GLN D 55 " ideal model delta sigma weight residual 118.79 113.25 5.54 1.21e+00 6.83e-01 2.09e+01 ... (remaining 19564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 7433 18.01 - 36.02: 891 36.02 - 54.03: 273 54.03 - 72.05: 56 72.05 - 90.06: 21 Dihedral angle restraints: 8674 sinusoidal: 3547 harmonic: 5127 Sorted by residual: dihedral pdb=" CB CYS D 3 " pdb=" SG CYS D 3 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual -86.00 -8.43 -77.57 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 98 " pdb=" SG CYS A 98 " pdb=" SG CYS E 3 " pdb=" CB CYS E 3 " ideal model delta sinusoidal sigma weight residual 93.00 154.60 -61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS A 3 " pdb=" SG CYS A 3 " pdb=" SG CYS B 98 " pdb=" CB CYS B 98 " ideal model delta sinusoidal sigma weight residual 93.00 146.33 -53.33 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 8671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1659 0.061 - 0.122: 477 0.122 - 0.183: 42 0.183 - 0.243: 4 0.243 - 0.304: 4 Chirality restraints: 2186 Sorted by residual: chirality pdb=" CA GLN D 55 " pdb=" N GLN D 55 " pdb=" C GLN D 55 " pdb=" CB GLN D 55 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA GLN E 55 " pdb=" N GLN E 55 " pdb=" C GLN E 55 " pdb=" CB GLN E 55 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA GLN B 55 " pdb=" N GLN B 55 " pdb=" C GLN B 55 " pdb=" CB GLN B 55 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2183 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 95 " -0.026 2.00e-02 2.50e+03 5.32e-02 2.83e+01 pdb=" C ASP E 95 " 0.092 2.00e-02 2.50e+03 pdb=" O ASP E 95 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU E 96 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 5 " -0.049 5.00e-02 4.00e+02 7.52e-02 9.06e+00 pdb=" N PRO E 6 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 6 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 6 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 73 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO E 74 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 74 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 74 " 0.039 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 306 2.65 - 3.21: 11802 3.21 - 3.77: 20774 3.77 - 4.34: 30341 4.34 - 4.90: 49658 Nonbonded interactions: 112881 Sorted by model distance: nonbonded pdb=" OE1 GLU B 154 " pdb=" NZ LYS B 258 " model vdw 2.084 3.120 nonbonded pdb=" O LYS C 127 " pdb=" OG1 THR C 139 " model vdw 2.139 3.040 nonbonded pdb=" O GLY A 115 " pdb=" OG SER A 118 " model vdw 2.165 3.040 nonbonded pdb=" OE1 GLN D 159 " pdb=" NZ LYS D 197 " model vdw 2.201 3.120 nonbonded pdb=" OG1 THR D 240 " pdb=" OG1 THR D 242 " model vdw 2.214 3.040 ... (remaining 112876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'B' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'C' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'D' and (resid 2 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 340)) selection = (chain 'E' and resid 2 through 340) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.190 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.009 0.093 14356 Z= 0.388 Angle : 0.942 10.241 19579 Z= 0.533 Chirality : 0.055 0.304 2186 Planarity : 0.007 0.075 2552 Dihedral : 17.781 90.058 5387 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.90 % Favored : 90.65 % Rotamer: Outliers : 9.18 % Allowed : 19.75 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.17), residues: 1786 helix: -3.41 (0.30), residues: 114 sheet: -0.77 (0.23), residues: 411 loop : -2.66 (0.15), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 40 TYR 0.017 0.002 TYR C 223 PHE 0.025 0.003 PHE B 290 TRP 0.020 0.003 TRP D 283 HIS 0.006 0.002 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00914 (14351) covalent geometry : angle 0.94182 (19569) SS BOND : bond 0.01113 ( 5) SS BOND : angle 1.67419 ( 10) hydrogen bonds : bond 0.20524 ( 368) hydrogen bonds : angle 9.15493 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 275 time to evaluate : 0.541 Fit side-chains REVERT: A 11 LYS cc_start: 0.6388 (mmtt) cc_final: 0.5631 (tttm) REVERT: A 183 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7908 (mmtm) REVERT: A 199 LYS cc_start: 0.8499 (mttm) cc_final: 0.8275 (mtpt) REVERT: A 238 GLN cc_start: 0.8153 (mt0) cc_final: 0.7815 (tt0) REVERT: A 249 ASP cc_start: 0.8311 (p0) cc_final: 0.8074 (p0) REVERT: A 283 TRP cc_start: 0.7896 (OUTLIER) cc_final: 0.6650 (m-90) REVERT: B 67 THR cc_start: 0.8285 (p) cc_final: 0.8059 (m) REVERT: B 91 MET cc_start: 0.8776 (mtm) cc_final: 0.8521 (mtm) REVERT: B 185 MET cc_start: 0.8868 (mtt) cc_final: 0.8552 (mtm) REVERT: B 238 GLN cc_start: 0.8102 (mt0) cc_final: 0.7707 (mm-40) REVERT: B 300 LYS cc_start: 0.6784 (mtmt) cc_final: 0.5786 (mmmt) REVERT: B 334 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.4001 (mt-10) REVERT: B 352 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8514 (mtt180) REVERT: C 40 ARG cc_start: 0.6068 (mtt90) cc_final: 0.5643 (tpp-160) REVERT: C 130 ASP cc_start: 0.7600 (t0) cc_final: 0.7244 (t0) REVERT: C 219 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5216 (tt0) REVERT: C 238 GLN cc_start: 0.8134 (mt0) cc_final: 0.7776 (mt0) REVERT: C 273 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8233 (ptt-90) REVERT: C 283 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: C 292 ILE cc_start: 0.9158 (mp) cc_final: 0.8874 (mp) REVERT: C 300 LYS cc_start: 0.6046 (mttt) cc_final: 0.5101 (mmtp) REVERT: C 350 MET cc_start: 0.7152 (tpt) cc_final: 0.6866 (tpt) REVERT: D 11 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8384 (tttm) REVERT: D 19 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6985 (pp20) REVERT: D 125 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8513 (t80) REVERT: D 315 ASN cc_start: 0.8282 (m-40) cc_final: 0.7880 (m110) REVERT: E 40 ARG cc_start: 0.6222 (mtm180) cc_final: 0.5779 (mmt-90) REVERT: E 71 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: E 154 GLU cc_start: 0.8622 (pt0) cc_final: 0.8348 (pt0) REVERT: E 218 ASN cc_start: 0.5051 (OUTLIER) cc_final: 0.4835 (m-40) REVERT: E 219 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.4609 (tp30) REVERT: E 238 GLN cc_start: 0.8328 (mt0) cc_final: 0.7984 (mt0) REVERT: E 321 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6582 (mp10) REVERT: E 361 LYS cc_start: 0.6102 (tmtt) cc_final: 0.5849 (tmtt) outliers start: 145 outliers final: 83 residues processed: 384 average time/residue: 0.5743 time to fit residues: 241.6365 Evaluate side-chains 341 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 245 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 145 GLN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 219 GLU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 218 ASN Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 321 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 93 ASN A 102 GLN A 126 ASN A 147 HIS ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 102 GLN B 123 HIS B 126 ASN B 147 HIS B 190 GLN B 282 HIS B 323 GLN B 331 GLN C 38 ASN C 88 GLN C 126 ASN C 147 HIS C 190 GLN C 282 HIS C 314 ASN C 315 ASN C 323 GLN C 331 GLN D 55 GLN D 88 GLN D 147 HIS D 301 ASN D 331 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 126 ASN E 147 HIS E 159 GLN E 190 GLN E 277 ASN E 282 HIS E 314 ASN E 315 ASN E 323 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.145670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.118544 restraints weight = 14764.190| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.56 r_work: 0.3007 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14356 Z= 0.154 Angle : 0.651 8.649 19579 Z= 0.339 Chirality : 0.045 0.171 2186 Planarity : 0.006 0.057 2552 Dihedral : 10.418 70.878 2084 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.94 % Favored : 92.95 % Rotamer: Outliers : 6.71 % Allowed : 22.22 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.18), residues: 1786 helix: -2.01 (0.46), residues: 100 sheet: -0.19 (0.24), residues: 399 loop : -2.06 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.010 0.001 TYR A 223 PHE 0.016 0.002 PHE E 290 TRP 0.011 0.002 TRP D 283 HIS 0.004 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00371 (14351) covalent geometry : angle 0.65025 (19569) SS BOND : bond 0.00406 ( 5) SS BOND : angle 1.05079 ( 10) hydrogen bonds : bond 0.03787 ( 368) hydrogen bonds : angle 5.73587 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 261 time to evaluate : 0.527 Fit side-chains REVERT: A 11 LYS cc_start: 0.6526 (mmtt) cc_final: 0.5268 (tttm) REVERT: A 41 MET cc_start: 0.8148 (ptm) cc_final: 0.7224 (ptp) REVERT: A 183 LYS cc_start: 0.8423 (mttt) cc_final: 0.7891 (mtmt) REVERT: A 199 LYS cc_start: 0.8556 (mttm) cc_final: 0.8338 (mtpt) REVERT: A 238 GLN cc_start: 0.8658 (mt0) cc_final: 0.8453 (mt0) REVERT: A 270 MET cc_start: 0.8961 (mmm) cc_final: 0.8568 (mmm) REVERT: A 283 TRP cc_start: 0.7999 (OUTLIER) cc_final: 0.6558 (m-10) REVERT: B 91 MET cc_start: 0.9215 (mtm) cc_final: 0.8947 (mtm) REVERT: B 127 LYS cc_start: 0.8353 (tttt) cc_final: 0.8093 (tttm) REVERT: B 238 GLN cc_start: 0.8512 (mt0) cc_final: 0.8106 (mp10) REVERT: B 300 LYS cc_start: 0.7101 (mtmt) cc_final: 0.5725 (mmmt) REVERT: B 334 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.4058 (mt-10) REVERT: B 352 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8627 (mtt180) REVERT: C 40 ARG cc_start: 0.5899 (mtt90) cc_final: 0.5670 (ttm170) REVERT: C 99 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7149 (t0) REVERT: C 199 LYS cc_start: 0.8821 (mttm) cc_final: 0.8424 (mptt) REVERT: D 11 LYS cc_start: 0.8921 (ttpt) cc_final: 0.8521 (tttm) REVERT: D 19 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7129 (pp20) REVERT: D 171 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: D 250 GLU cc_start: 0.7764 (mp0) cc_final: 0.7541 (mp0) REVERT: E 28 ASP cc_start: 0.8013 (m-30) cc_final: 0.7718 (m-30) REVERT: E 40 ARG cc_start: 0.6219 (mtm180) cc_final: 0.5221 (mmt90) REVERT: E 154 GLU cc_start: 0.9076 (pt0) cc_final: 0.8717 (pt0) REVERT: E 161 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8153 (tp) REVERT: E 238 GLN cc_start: 0.8479 (mt0) cc_final: 0.8184 (mp10) REVERT: E 299 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (m) REVERT: E 305 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8374 (ttm) REVERT: E 321 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6437 (mp10) outliers start: 106 outliers final: 46 residues processed: 336 average time/residue: 0.5740 time to fit residues: 211.6987 Evaluate side-chains 292 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 321 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.140444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.110282 restraints weight = 14817.058| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.75 r_work: 0.2851 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14356 Z= 0.160 Angle : 0.641 7.840 19579 Z= 0.329 Chirality : 0.046 0.175 2186 Planarity : 0.006 0.054 2552 Dihedral : 8.626 68.567 1979 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.01 % Favored : 91.88 % Rotamer: Outliers : 6.65 % Allowed : 23.10 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.19), residues: 1786 helix: -1.53 (0.49), residues: 100 sheet: 0.13 (0.25), residues: 399 loop : -1.81 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 40 TYR 0.013 0.001 TYR D 223 PHE 0.016 0.002 PHE B 290 TRP 0.011 0.002 TRP D 283 HIS 0.003 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00391 (14351) covalent geometry : angle 0.64067 (19569) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.85988 ( 10) hydrogen bonds : bond 0.03393 ( 368) hydrogen bonds : angle 5.39979 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 238 time to evaluate : 0.534 Fit side-chains REVERT: A 11 LYS cc_start: 0.6660 (mmtt) cc_final: 0.5426 (tttm) REVERT: A 41 MET cc_start: 0.8033 (ptm) cc_final: 0.7093 (ptp) REVERT: A 183 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7871 (mtmt) REVERT: A 199 LYS cc_start: 0.8537 (mttm) cc_final: 0.8312 (mtpt) REVERT: A 238 GLN cc_start: 0.8663 (mt0) cc_final: 0.8414 (mt0) REVERT: A 270 MET cc_start: 0.8907 (mmm) cc_final: 0.8420 (mmm) REVERT: A 283 TRP cc_start: 0.7952 (OUTLIER) cc_final: 0.6479 (m-10) REVERT: B 91 MET cc_start: 0.9186 (mtm) cc_final: 0.8959 (mtm) REVERT: B 127 LYS cc_start: 0.8151 (tttt) cc_final: 0.7906 (tttm) REVERT: B 238 GLN cc_start: 0.8465 (mt0) cc_final: 0.8087 (mp10) REVERT: B 300 LYS cc_start: 0.6922 (mtmt) cc_final: 0.5536 (mmmt) REVERT: B 334 GLU cc_start: 0.5622 (OUTLIER) cc_final: 0.3967 (mt-10) REVERT: C 34 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: C 99 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6952 (t0) REVERT: C 184 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: D 11 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8468 (tttm) REVERT: D 19 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7042 (pp20) REVERT: D 238 GLN cc_start: 0.8579 (mt0) cc_final: 0.8204 (mp10) REVERT: E 28 ASP cc_start: 0.7979 (m-30) cc_final: 0.7703 (m-30) REVERT: E 40 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.5933 (mmt-90) REVERT: E 71 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: E 154 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8629 (pt0) REVERT: E 161 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8128 (tp) REVERT: E 238 GLN cc_start: 0.8471 (mt0) cc_final: 0.8212 (mp10) REVERT: E 299 VAL cc_start: 0.8744 (t) cc_final: 0.8524 (m) REVERT: E 300 LYS cc_start: 0.8448 (tptt) cc_final: 0.8027 (mmmt) REVERT: E 321 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6451 (mp10) REVERT: E 325 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.7367 (mpp) REVERT: E 361 LYS cc_start: 0.6398 (tmtt) cc_final: 0.6059 (tmtt) outliers start: 105 outliers final: 53 residues processed: 314 average time/residue: 0.5628 time to fit residues: 194.0983 Evaluate side-chains 292 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 90 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.138696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108356 restraints weight = 14779.949| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.76 r_work: 0.2821 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14356 Z= 0.196 Angle : 0.671 7.980 19579 Z= 0.343 Chirality : 0.047 0.205 2186 Planarity : 0.006 0.054 2552 Dihedral : 8.423 68.925 1969 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 7.15 % Allowed : 23.16 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.19), residues: 1786 helix: -1.29 (0.50), residues: 100 sheet: 0.25 (0.25), residues: 396 loop : -1.69 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 40 TYR 0.014 0.002 TYR D 223 PHE 0.017 0.002 PHE B 290 TRP 0.013 0.002 TRP B 283 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00487 (14351) covalent geometry : angle 0.67081 (19569) SS BOND : bond 0.00169 ( 5) SS BOND : angle 0.99271 ( 10) hydrogen bonds : bond 0.03378 ( 368) hydrogen bonds : angle 5.36048 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 235 time to evaluate : 0.527 Fit side-chains REVERT: A 11 LYS cc_start: 0.6619 (mmtt) cc_final: 0.5431 (tttm) REVERT: A 41 MET cc_start: 0.8030 (ptm) cc_final: 0.7083 (ptp) REVERT: A 183 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7834 (mtmt) REVERT: A 199 LYS cc_start: 0.8600 (mttm) cc_final: 0.8377 (mtpt) REVERT: A 238 GLN cc_start: 0.8679 (mt0) cc_final: 0.8424 (mt0) REVERT: A 270 MET cc_start: 0.8943 (mmm) cc_final: 0.8417 (mmm) REVERT: A 283 TRP cc_start: 0.7989 (OUTLIER) cc_final: 0.6528 (m-10) REVERT: B 127 LYS cc_start: 0.8153 (tttt) cc_final: 0.7902 (tttm) REVERT: B 238 GLN cc_start: 0.8520 (mt0) cc_final: 0.8082 (mp10) REVERT: B 300 LYS cc_start: 0.6915 (mtmt) cc_final: 0.5518 (mmmt) REVERT: B 334 GLU cc_start: 0.5947 (OUTLIER) cc_final: 0.4147 (mt-10) REVERT: C 34 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: C 48 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7546 (mp0) REVERT: C 99 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6975 (t0) REVERT: D 11 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8465 (tttm) REVERT: D 19 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7133 (pp20) REVERT: D 48 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7142 (mm-30) REVERT: D 161 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8386 (tt) REVERT: D 238 GLN cc_start: 0.8566 (mt0) cc_final: 0.8215 (mp10) REVERT: E 28 ASP cc_start: 0.7995 (m-30) cc_final: 0.7735 (m-30) REVERT: E 40 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.5883 (mmt-90) REVERT: E 71 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6965 (mm-30) REVERT: E 154 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: E 161 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8185 (tp) REVERT: E 238 GLN cc_start: 0.8579 (mt0) cc_final: 0.8315 (mp10) REVERT: E 299 VAL cc_start: 0.8760 (t) cc_final: 0.8467 (m) REVERT: E 300 LYS cc_start: 0.8439 (tptt) cc_final: 0.8008 (mmmt) REVERT: E 321 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6462 (mp10) outliers start: 113 outliers final: 69 residues processed: 312 average time/residue: 0.5597 time to fit residues: 191.9522 Evaluate side-chains 310 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 229 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 363 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 301 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.141408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110856 restraints weight = 14761.016| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.74 r_work: 0.2864 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14356 Z= 0.139 Angle : 0.607 7.582 19579 Z= 0.311 Chirality : 0.045 0.176 2186 Planarity : 0.005 0.049 2552 Dihedral : 7.868 67.297 1966 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.50 % Favored : 92.39 % Rotamer: Outliers : 6.52 % Allowed : 23.80 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.19), residues: 1786 helix: -0.77 (0.54), residues: 93 sheet: 0.27 (0.25), residues: 401 loop : -1.50 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 276 TYR 0.012 0.001 TYR D 223 PHE 0.014 0.002 PHE E 290 TRP 0.013 0.001 TRP B 283 HIS 0.005 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00342 (14351) covalent geometry : angle 0.60670 (19569) SS BOND : bond 0.00156 ( 5) SS BOND : angle 0.66275 ( 10) hydrogen bonds : bond 0.02956 ( 368) hydrogen bonds : angle 5.09312 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 237 time to evaluate : 0.653 Fit side-chains REVERT: A 11 LYS cc_start: 0.6437 (mmtt) cc_final: 0.5325 (tttm) REVERT: A 41 MET cc_start: 0.7950 (ptm) cc_final: 0.7032 (ptp) REVERT: A 51 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7938 (m) REVERT: A 183 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7817 (mtmt) REVERT: A 199 LYS cc_start: 0.8519 (mttm) cc_final: 0.8290 (mtpt) REVERT: A 238 GLN cc_start: 0.8649 (mt0) cc_final: 0.8413 (mt0) REVERT: A 270 MET cc_start: 0.8949 (mmm) cc_final: 0.8434 (mmm) REVERT: A 283 TRP cc_start: 0.7934 (OUTLIER) cc_final: 0.6457 (m-10) REVERT: B 41 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7795 (mmm) REVERT: B 130 ASP cc_start: 0.7775 (t70) cc_final: 0.7244 (t0) REVERT: B 238 GLN cc_start: 0.8557 (mt0) cc_final: 0.8143 (mp10) REVERT: B 300 LYS cc_start: 0.6922 (mtmt) cc_final: 0.5533 (mmmt) REVERT: B 328 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: B 334 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.4075 (mt-10) REVERT: B 352 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8584 (mtt180) REVERT: C 48 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7449 (mp0) REVERT: C 199 LYS cc_start: 0.8740 (mttm) cc_final: 0.8400 (mptt) REVERT: C 258 LYS cc_start: 0.7917 (ptpt) cc_final: 0.6790 (mmtp) REVERT: C 295 ARG cc_start: 0.8938 (ptt180) cc_final: 0.8721 (ptt180) REVERT: D 11 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8483 (tttm) REVERT: D 19 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7108 (pp20) REVERT: D 48 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 161 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8266 (tt) REVERT: D 238 GLN cc_start: 0.8551 (mt0) cc_final: 0.8196 (mp10) REVERT: E 28 ASP cc_start: 0.7976 (m-30) cc_final: 0.7708 (m-30) REVERT: E 40 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.6050 (mmt-90) REVERT: E 71 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: E 154 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8600 (pt0) REVERT: E 161 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8129 (tp) REVERT: E 238 GLN cc_start: 0.8494 (mt0) cc_final: 0.8226 (mp10) REVERT: E 299 VAL cc_start: 0.8613 (t) cc_final: 0.8406 (m) REVERT: E 300 LYS cc_start: 0.8452 (tptt) cc_final: 0.8012 (mmmt) REVERT: E 321 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6456 (mp10) outliers start: 103 outliers final: 55 residues processed: 312 average time/residue: 0.5522 time to fit residues: 189.3369 Evaluate side-chains 297 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 153 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 158 optimal weight: 0.0570 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 331 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.138116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.107876 restraints weight = 14789.445| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.75 r_work: 0.2811 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14356 Z= 0.228 Angle : 0.692 8.343 19579 Z= 0.353 Chirality : 0.048 0.222 2186 Planarity : 0.006 0.052 2552 Dihedral : 7.986 69.842 1958 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.29 % Favored : 91.60 % Rotamer: Outliers : 6.58 % Allowed : 23.80 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.19), residues: 1786 helix: -1.36 (0.48), residues: 114 sheet: 0.30 (0.26), residues: 400 loop : -1.58 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 40 TYR 0.014 0.002 TYR D 223 PHE 0.019 0.002 PHE B 290 TRP 0.014 0.002 TRP D 283 HIS 0.005 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00568 (14351) covalent geometry : angle 0.69170 (19569) SS BOND : bond 0.00151 ( 5) SS BOND : angle 1.24025 ( 10) hydrogen bonds : bond 0.03375 ( 368) hydrogen bonds : angle 5.32058 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 230 time to evaluate : 0.540 Fit side-chains REVERT: A 11 LYS cc_start: 0.6629 (mmtt) cc_final: 0.5462 (tttm) REVERT: A 41 MET cc_start: 0.7929 (ptm) cc_final: 0.7468 (ptm) REVERT: A 183 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7823 (mtmt) REVERT: A 238 GLN cc_start: 0.8713 (mt0) cc_final: 0.8461 (mt0) REVERT: A 270 MET cc_start: 0.8935 (mmm) cc_final: 0.8430 (mmm) REVERT: A 283 TRP cc_start: 0.8001 (OUTLIER) cc_final: 0.6635 (m-10) REVERT: A 316 MET cc_start: 0.2939 (mmm) cc_final: 0.2652 (mmm) REVERT: B 238 GLN cc_start: 0.8561 (mt0) cc_final: 0.8212 (mp10) REVERT: B 300 LYS cc_start: 0.6959 (mtmt) cc_final: 0.5521 (mmmt) REVERT: B 334 GLU cc_start: 0.5996 (OUTLIER) cc_final: 0.4192 (mt-10) REVERT: C 48 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7506 (mp0) REVERT: C 283 TRP cc_start: 0.8307 (OUTLIER) cc_final: 0.7869 (m-90) REVERT: C 295 ARG cc_start: 0.8978 (ptt180) cc_final: 0.8743 (ptt180) REVERT: D 11 LYS cc_start: 0.8924 (ttpt) cc_final: 0.8471 (tttm) REVERT: D 19 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: D 161 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8426 (tt) REVERT: D 238 GLN cc_start: 0.8579 (mt0) cc_final: 0.8219 (mp10) REVERT: E 28 ASP cc_start: 0.7909 (m-30) cc_final: 0.7678 (m-30) REVERT: E 40 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.5991 (mmt-90) REVERT: E 71 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6859 (mm-30) REVERT: E 154 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8608 (pt0) REVERT: E 161 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8237 (tp) REVERT: E 238 GLN cc_start: 0.8569 (mt0) cc_final: 0.8322 (mp10) REVERT: E 299 VAL cc_start: 0.8619 (t) cc_final: 0.8362 (m) REVERT: E 300 LYS cc_start: 0.8443 (tptt) cc_final: 0.8010 (tmtm) REVERT: E 321 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6463 (mp10) outliers start: 104 outliers final: 66 residues processed: 302 average time/residue: 0.5930 time to fit residues: 196.0793 Evaluate side-chains 302 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 225 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 17 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.140690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110457 restraints weight = 14747.076| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.73 r_work: 0.2856 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14356 Z= 0.146 Angle : 0.612 7.367 19579 Z= 0.314 Chirality : 0.045 0.189 2186 Planarity : 0.005 0.055 2552 Dihedral : 7.634 69.159 1958 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 6.20 % Allowed : 23.99 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1786 helix: -0.91 (0.52), residues: 101 sheet: 0.31 (0.26), residues: 398 loop : -1.48 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.011 0.001 TYR D 223 PHE 0.014 0.002 PHE E 290 TRP 0.013 0.002 TRP B 283 HIS 0.004 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00361 (14351) covalent geometry : angle 0.61163 (19569) SS BOND : bond 0.00131 ( 5) SS BOND : angle 0.84132 ( 10) hydrogen bonds : bond 0.02966 ( 368) hydrogen bonds : angle 5.09423 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 229 time to evaluate : 0.542 Fit side-chains REVERT: A 11 LYS cc_start: 0.6636 (mmtt) cc_final: 0.5467 (tttm) REVERT: A 41 MET cc_start: 0.7855 (ptm) cc_final: 0.7330 (ptm) REVERT: A 172 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: A 183 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7850 (mtmt) REVERT: A 238 GLN cc_start: 0.8641 (mt0) cc_final: 0.8399 (mt0) REVERT: A 270 MET cc_start: 0.8921 (mmm) cc_final: 0.8418 (mmm) REVERT: A 283 TRP cc_start: 0.7967 (OUTLIER) cc_final: 0.6511 (m-10) REVERT: A 300 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7675 (mtpt) REVERT: A 316 MET cc_start: 0.2847 (mmm) cc_final: 0.2525 (mmm) REVERT: B 238 GLN cc_start: 0.8565 (mt0) cc_final: 0.8163 (mp10) REVERT: B 300 LYS cc_start: 0.6928 (mtmt) cc_final: 0.5528 (mmmt) REVERT: B 334 GLU cc_start: 0.5689 (OUTLIER) cc_final: 0.4086 (mt-10) REVERT: B 352 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8541 (mtt180) REVERT: C 258 LYS cc_start: 0.7969 (ptpt) cc_final: 0.6793 (mmtp) REVERT: C 295 ARG cc_start: 0.8942 (ptt180) cc_final: 0.8709 (ptt180) REVERT: D 11 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8473 (tttm) REVERT: D 19 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7071 (pp20) REVERT: D 48 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 161 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8291 (tt) REVERT: D 176 THR cc_start: 0.8670 (m) cc_final: 0.8182 (p) REVERT: D 238 GLN cc_start: 0.8533 (mt0) cc_final: 0.8180 (mp10) REVERT: D 312 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8258 (tp) REVERT: E 28 ASP cc_start: 0.7923 (m-30) cc_final: 0.7688 (m-30) REVERT: E 40 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5647 (mmt90) REVERT: E 71 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: E 154 GLU cc_start: 0.8948 (pt0) cc_final: 0.8573 (pt0) REVERT: E 161 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8117 (tp) REVERT: E 238 GLN cc_start: 0.8460 (mt0) cc_final: 0.8192 (mp10) REVERT: E 250 GLU cc_start: 0.7700 (tt0) cc_final: 0.7334 (tt0) REVERT: E 300 LYS cc_start: 0.8422 (tptt) cc_final: 0.7990 (tmtm) REVERT: E 321 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6440 (mp10) outliers start: 98 outliers final: 65 residues processed: 302 average time/residue: 0.5849 time to fit residues: 194.5123 Evaluate side-chains 305 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 227 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 9 optimal weight: 6.9990 chunk 95 optimal weight: 0.0010 chunk 44 optimal weight: 0.9980 chunk 158 optimal weight: 0.2980 chunk 30 optimal weight: 0.0270 chunk 119 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 69 optimal weight: 0.0470 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 315 ASN D 55 GLN D 77 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN E 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.147462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117508 restraints weight = 14793.174| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.72 r_work: 0.2954 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14356 Z= 0.096 Angle : 0.544 6.480 19579 Z= 0.280 Chirality : 0.042 0.158 2186 Planarity : 0.005 0.042 2552 Dihedral : 6.861 62.467 1958 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.78 % Rotamer: Outliers : 3.73 % Allowed : 26.52 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1786 helix: -0.74 (0.53), residues: 101 sheet: 0.31 (0.26), residues: 382 loop : -1.31 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.011 0.001 TYR B 289 PHE 0.012 0.001 PHE B 149 TRP 0.014 0.002 TRP D 82 HIS 0.003 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00231 (14351) covalent geometry : angle 0.54445 (19569) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.59429 ( 10) hydrogen bonds : bond 0.02545 ( 368) hydrogen bonds : angle 4.62923 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.531 Fit side-chains REVERT: A 11 LYS cc_start: 0.6621 (mmtt) cc_final: 0.5477 (tttm) REVERT: A 41 MET cc_start: 0.7847 (ptm) cc_final: 0.7056 (ptt) REVERT: A 64 ASN cc_start: 0.8609 (p0) cc_final: 0.8388 (p0) REVERT: A 182 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7711 (mmpt) REVERT: A 199 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8137 (mmtt) REVERT: A 238 GLN cc_start: 0.8633 (mt0) cc_final: 0.8391 (mt0) REVERT: A 270 MET cc_start: 0.8902 (mmm) cc_final: 0.8355 (mmm) REVERT: A 283 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.6373 (m-10) REVERT: A 316 MET cc_start: 0.2567 (mmm) cc_final: 0.2186 (mmm) REVERT: B 238 GLN cc_start: 0.8567 (mt0) cc_final: 0.8141 (mp10) REVERT: B 300 LYS cc_start: 0.6911 (mtmt) cc_final: 0.5484 (mmmt) REVERT: B 352 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8408 (mtt90) REVERT: C 40 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7653 (mmt90) REVERT: C 48 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7261 (mp0) REVERT: C 101 LEU cc_start: 0.7990 (tt) cc_final: 0.7654 (tp) REVERT: C 127 LYS cc_start: 0.8424 (tttt) cc_final: 0.8183 (ttpt) REVERT: C 183 LYS cc_start: 0.8262 (pttm) cc_final: 0.8043 (pttt) REVERT: C 258 LYS cc_start: 0.7459 (ptpt) cc_final: 0.6544 (mmtp) REVERT: D 11 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8486 (tttm) REVERT: D 48 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7189 (mm-30) REVERT: D 176 THR cc_start: 0.8450 (m) cc_final: 0.7919 (p) REVERT: D 180 ILE cc_start: 0.8886 (mm) cc_final: 0.8661 (mp) REVERT: D 238 GLN cc_start: 0.8539 (mt0) cc_final: 0.8188 (mp10) REVERT: E 28 ASP cc_start: 0.7903 (m-30) cc_final: 0.7660 (m-30) REVERT: E 40 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.5668 (mmt90) REVERT: E 154 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8532 (pt0) REVERT: E 161 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8086 (tt) REVERT: E 238 GLN cc_start: 0.8417 (mt0) cc_final: 0.8179 (mp10) REVERT: E 250 GLU cc_start: 0.7685 (tt0) cc_final: 0.7324 (tt0) REVERT: E 300 LYS cc_start: 0.8423 (tptt) cc_final: 0.8008 (mmmt) outliers start: 59 outliers final: 33 residues processed: 292 average time/residue: 0.5679 time to fit residues: 182.7645 Evaluate side-chains 265 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 44 optimal weight: 4.9990 chunk 139 optimal weight: 0.0470 chunk 174 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN D 55 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.138624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.108354 restraints weight = 14763.906| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.75 r_work: 0.2838 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14356 Z= 0.227 Angle : 0.691 7.428 19579 Z= 0.353 Chirality : 0.048 0.234 2186 Planarity : 0.006 0.059 2552 Dihedral : 6.939 59.908 1945 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 91.99 % Rotamer: Outliers : 4.05 % Allowed : 26.71 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.20), residues: 1786 helix: -0.94 (0.53), residues: 101 sheet: 0.38 (0.26), residues: 400 loop : -1.35 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 40 TYR 0.016 0.002 TYR B 223 PHE 0.020 0.003 PHE E 290 TRP 0.013 0.002 TRP B 283 HIS 0.004 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00563 (14351) covalent geometry : angle 0.69119 (19569) SS BOND : bond 0.00185 ( 5) SS BOND : angle 1.06107 ( 10) hydrogen bonds : bond 0.03286 ( 368) hydrogen bonds : angle 5.24075 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 229 time to evaluate : 0.540 Fit side-chains REVERT: A 11 LYS cc_start: 0.6836 (mmtt) cc_final: 0.5462 (tttp) REVERT: A 41 MET cc_start: 0.8064 (ptm) cc_final: 0.7545 (ptm) REVERT: A 238 GLN cc_start: 0.8918 (mt0) cc_final: 0.8682 (mt0) REVERT: A 270 MET cc_start: 0.9034 (mmm) cc_final: 0.8525 (mmm) REVERT: A 283 TRP cc_start: 0.8136 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: A 316 MET cc_start: 0.2845 (mmm) cc_final: 0.2441 (mmm) REVERT: B 41 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8042 (mmt) REVERT: B 67 THR cc_start: 0.8462 (p) cc_final: 0.7956 (m) REVERT: B 102 GLN cc_start: 0.8924 (pt0) cc_final: 0.8574 (pt0) REVERT: B 238 GLN cc_start: 0.8757 (mt0) cc_final: 0.8279 (mp10) REVERT: B 300 LYS cc_start: 0.7156 (mtmt) cc_final: 0.5599 (mmmt) REVERT: C 183 LYS cc_start: 0.8343 (pttm) cc_final: 0.8142 (pttt) REVERT: C 199 LYS cc_start: 0.8681 (mptt) cc_final: 0.8205 (mmmt) REVERT: C 258 LYS cc_start: 0.8091 (ptpt) cc_final: 0.6971 (mptt) REVERT: C 295 ARG cc_start: 0.8983 (ptt180) cc_final: 0.8751 (ptt180) REVERT: D 11 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8474 (tttm) REVERT: D 48 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7409 (mm-30) REVERT: D 238 GLN cc_start: 0.8709 (mt0) cc_final: 0.8377 (mp10) REVERT: E 28 ASP cc_start: 0.8084 (m-30) cc_final: 0.7819 (m-30) REVERT: E 40 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5894 (mmt-90) REVERT: E 91 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7880 (mmt) REVERT: E 154 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8793 (pt0) REVERT: E 161 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8368 (tp) REVERT: E 238 GLN cc_start: 0.8737 (mt0) cc_final: 0.8480 (mp10) REVERT: E 250 GLU cc_start: 0.7887 (tt0) cc_final: 0.7547 (tt0) REVERT: E 300 LYS cc_start: 0.8603 (tptt) cc_final: 0.8176 (mmmt) REVERT: E 319 GLN cc_start: 0.7149 (mm-40) cc_final: 0.6941 (mp10) REVERT: E 326 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7293 (pp20) outliers start: 64 outliers final: 48 residues processed: 274 average time/residue: 0.5796 time to fit residues: 174.3597 Evaluate side-chains 282 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 SER Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 167 optimal weight: 0.3980 chunk 81 optimal weight: 0.4980 chunk 172 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 chunk 114 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 226 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.144831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.115017 restraints weight = 14869.833| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.70 r_work: 0.2918 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14356 Z= 0.103 Angle : 0.561 9.172 19579 Z= 0.289 Chirality : 0.043 0.170 2186 Planarity : 0.005 0.061 2552 Dihedral : 6.322 59.210 1944 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.66 % Favored : 93.28 % Rotamer: Outliers : 3.23 % Allowed : 27.28 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.20), residues: 1786 helix: -0.75 (0.52), residues: 101 sheet: 0.37 (0.26), residues: 382 loop : -1.26 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.011 0.001 TYR D 289 PHE 0.011 0.001 PHE E 290 TRP 0.013 0.002 TRP D 82 HIS 0.004 0.001 HIS D 282 Details of bonding type rmsd covalent geometry : bond 0.00251 (14351) covalent geometry : angle 0.56100 (19569) SS BOND : bond 0.00180 ( 5) SS BOND : angle 0.64715 ( 10) hydrogen bonds : bond 0.02670 ( 368) hydrogen bonds : angle 4.77544 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.507 Fit side-chains REVERT: A 11 LYS cc_start: 0.6567 (mmtt) cc_final: 0.5443 (tttm) REVERT: A 41 MET cc_start: 0.7830 (ptm) cc_final: 0.7000 (ptt) REVERT: A 64 ASN cc_start: 0.8610 (p0) cc_final: 0.8336 (p0) REVERT: A 182 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7746 (mmpt) REVERT: A 199 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8154 (mmtt) REVERT: A 238 GLN cc_start: 0.8632 (mt0) cc_final: 0.8383 (mt0) REVERT: A 270 MET cc_start: 0.8865 (mmm) cc_final: 0.8304 (mmm) REVERT: A 283 TRP cc_start: 0.7885 (OUTLIER) cc_final: 0.6462 (m-10) REVERT: A 316 MET cc_start: 0.2975 (mmm) cc_final: 0.2555 (mmm) REVERT: B 41 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7527 (mmm) REVERT: B 67 THR cc_start: 0.8452 (p) cc_final: 0.7939 (m) REVERT: B 238 GLN cc_start: 0.8577 (mt0) cc_final: 0.8141 (mp10) REVERT: B 300 LYS cc_start: 0.6902 (mtmt) cc_final: 0.5517 (mmmt) REVERT: C 183 LYS cc_start: 0.8168 (pttm) cc_final: 0.7947 (pttt) REVERT: C 258 LYS cc_start: 0.7568 (ptpt) cc_final: 0.6623 (mmtp) REVERT: C 295 ARG cc_start: 0.8800 (ptt180) cc_final: 0.8534 (ptt180) REVERT: D 11 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8472 (tttm) REVERT: D 48 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7316 (mm-30) REVERT: D 130 ASP cc_start: 0.7452 (t0) cc_final: 0.7071 (t0) REVERT: D 176 THR cc_start: 0.8532 (m) cc_final: 0.7993 (p) REVERT: D 238 GLN cc_start: 0.8515 (mt0) cc_final: 0.8154 (mp10) REVERT: E 28 ASP cc_start: 0.7894 (m-30) cc_final: 0.7680 (m-30) REVERT: E 40 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6009 (mmt-90) REVERT: E 154 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: E 161 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8093 (tt) REVERT: E 238 GLN cc_start: 0.8458 (mt0) cc_final: 0.8197 (mp10) REVERT: E 250 GLU cc_start: 0.7655 (tt0) cc_final: 0.7288 (tt0) REVERT: E 300 LYS cc_start: 0.8379 (tptt) cc_final: 0.7981 (mmmt) outliers start: 51 outliers final: 37 residues processed: 273 average time/residue: 0.5981 time to fit residues: 179.2197 Evaluate side-chains 271 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 110 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.141297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.110885 restraints weight = 14845.612| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.76 r_work: 0.2871 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14356 Z= 0.156 Angle : 0.618 8.999 19579 Z= 0.317 Chirality : 0.045 0.199 2186 Planarity : 0.005 0.061 2552 Dihedral : 6.518 58.839 1944 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.56 % Favored : 92.33 % Rotamer: Outliers : 3.54 % Allowed : 27.15 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.20), residues: 1786 helix: -0.76 (0.53), residues: 101 sheet: 0.40 (0.26), residues: 394 loop : -1.24 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 40 TYR 0.013 0.001 TYR B 223 PHE 0.015 0.002 PHE E 290 TRP 0.011 0.001 TRP B 283 HIS 0.005 0.001 HIS D 282 Details of bonding type rmsd covalent geometry : bond 0.00385 (14351) covalent geometry : angle 0.61836 (19569) SS BOND : bond 0.00106 ( 5) SS BOND : angle 0.81701 ( 10) hydrogen bonds : bond 0.02897 ( 368) hydrogen bonds : angle 4.96802 ( 1224) =============================================================================== Job complete usr+sys time: 5460.65 seconds wall clock time: 93 minutes 38.12 seconds (5618.12 seconds total)