Starting phenix.real_space_refine on Thu Jul 31 15:35:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k25_22643/07_2025/7k25_22643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k25_22643/07_2025/7k25_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7k25_22643/07_2025/7k25_22643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k25_22643/07_2025/7k25_22643.map" model { file = "/net/cci-nas-00/data/ceres_data/7k25_22643/07_2025/7k25_22643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k25_22643/07_2025/7k25_22643.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.90, per 1000 atoms: 0.64 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: 3.07 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.93 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: 4.43 Time building geometry restraints manager: 3.74 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.260 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.003 TRP D 283 HIS 0.006 0.002 HIS D 281 PHE 0.025 0.003 PHE B 290 TYR 0.017 0.002 TYR C 223 ARG 0.007 0.001 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.20524 ( 368) hydrogen bonds : angle 9.15493 ( 1224) SS BOND : bond 0.01113 ( 5) SS BOND : angle 1.67419 ( 10) covalent geometry : bond 0.00914 (14351) covalent geometry : angle 0.94182 (19569) *********************** 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 : 1.645 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: A 331 GLN cc_start: 0.8680 (mt0) cc_final: 0.8460 (mt0) 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: 0.5778 (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: 1.1888 time to fit residues: 502.4004 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 : 1.569 ------------------------------------------------------------------------------- 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 149 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 74 optimal weight: 0.0770 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.143858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.112891 restraints weight = 14455.204| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.76 r_work: 0.2900 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14356 Z= 0.124 Angle : 0.611 8.206 19579 Z= 0.318 Chirality : 0.044 0.160 2186 Planarity : 0.006 0.054 2552 Dihedral : 9.895 69.977 2084 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 5.70 % Allowed : 22.47 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.19), residues: 1786 helix: -1.92 (0.46), residues: 100 sheet: -0.17 (0.25), residues: 397 loop : -2.00 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 82 HIS 0.003 0.001 HIS B 123 PHE 0.013 0.001 PHE E 290 TYR 0.009 0.001 TYR C 278 ARG 0.005 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03421 ( 368) hydrogen bonds : angle 5.54451 ( 1224) SS BOND : bond 0.00822 ( 5) SS BOND : angle 1.00050 ( 10) covalent geometry : bond 0.00291 (14351) covalent geometry : angle 0.61071 (19569) *********************** 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 357 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 267 time to evaluate : 1.809 Fit side-chains REVERT: A 11 LYS cc_start: 0.6432 (mmtt) cc_final: 0.5253 (tttm) REVERT: A 41 MET cc_start: 0.7969 (ptm) cc_final: 0.7261 (ptp) REVERT: A 127 LYS cc_start: 0.8433 (tttt) cc_final: 0.8229 (ttpt) REVERT: A 183 LYS cc_start: 0.8391 (mttt) cc_final: 0.7894 (mtmt) REVERT: A 199 LYS cc_start: 0.8458 (mttm) cc_final: 0.8246 (mtpt) REVERT: A 238 GLN cc_start: 0.8628 (mt0) cc_final: 0.8399 (mt0) REVERT: A 249 ASP cc_start: 0.8689 (p0) cc_final: 0.8485 (p0) REVERT: A 283 TRP cc_start: 0.7876 (OUTLIER) cc_final: 0.6327 (m-10) REVERT: A 300 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7727 (mtpt) REVERT: B 91 MET cc_start: 0.9198 (mtm) cc_final: 0.8939 (mtm) REVERT: B 127 LYS cc_start: 0.8128 (tttt) cc_final: 0.7858 (tttm) REVERT: B 183 LYS cc_start: 0.8549 (mptt) cc_final: 0.8217 (mptp) REVERT: B 238 GLN cc_start: 0.8440 (mt0) cc_final: 0.8045 (mp10) REVERT: B 300 LYS cc_start: 0.6898 (mtmt) cc_final: 0.5565 (mmmt) REVERT: B 334 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.3880 (mt-10) REVERT: C 99 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7015 (t0) REVERT: C 127 LYS cc_start: 0.8493 (tttt) cc_final: 0.8268 (tttm) REVERT: C 199 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8373 (mptt) REVERT: D 11 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8482 (tttm) REVERT: D 19 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7035 (pp20) REVERT: D 250 GLU cc_start: 0.7570 (mp0) cc_final: 0.7326 (mp0) REVERT: E 20 VAL cc_start: 0.8425 (t) cc_final: 0.8055 (m) REVERT: E 28 ASP cc_start: 0.7971 (m-30) cc_final: 0.7690 (m-30) REVERT: E 40 ARG cc_start: 0.6075 (mtm180) cc_final: 0.5188 (mmt90) REVERT: E 154 GLU cc_start: 0.8958 (pt0) cc_final: 0.8582 (pt0) REVERT: E 161 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8063 (tp) REVERT: E 238 GLN cc_start: 0.8482 (mt0) cc_final: 0.8199 (mp10) REVERT: E 321 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6364 (mp10) REVERT: E 361 LYS cc_start: 0.5967 (tmtt) cc_final: 0.5513 (tmtt) outliers start: 90 outliers final: 33 residues processed: 333 average time/residue: 1.2876 time to fit residues: 469.4048 Evaluate side-chains 276 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain A residue 138 SER 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 300 LYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 328 GLU 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 350 MET 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 175 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 199 LYS 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 116 SER 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 21 LEU Chi-restraints excluded: chain E residue 116 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 321 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 174 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 159 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN E 55 GLN E 93 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.138999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.108766 restraints weight = 14547.639| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.72 r_work: 0.2829 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14356 Z= 0.203 Angle : 0.679 8.067 19579 Z= 0.348 Chirality : 0.047 0.187 2186 Planarity : 0.006 0.053 2552 Dihedral : 8.453 68.746 1966 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 91.99 % Rotamer: Outliers : 6.14 % Allowed : 23.35 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.19), residues: 1786 helix: -1.60 (0.48), residues: 100 sheet: 0.13 (0.25), residues: 396 loop : -1.83 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 283 HIS 0.004 0.001 HIS B 282 PHE 0.019 0.002 PHE B 290 TYR 0.015 0.002 TYR D 223 ARG 0.006 0.001 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 368) hydrogen bonds : angle 5.49575 ( 1224) SS BOND : bond 0.00209 ( 5) SS BOND : angle 1.01596 ( 10) covalent geometry : bond 0.00502 (14351) covalent geometry : angle 0.67856 (19569) *********************** 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 335 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 238 time to evaluate : 1.578 Fit side-chains REVERT: A 11 LYS cc_start: 0.6616 (mmtt) cc_final: 0.5429 (tttp) REVERT: A 41 MET cc_start: 0.8056 (ptm) cc_final: 0.7095 (ptp) REVERT: A 183 LYS cc_start: 0.8435 (mttt) cc_final: 0.7933 (mtmt) REVERT: A 199 LYS cc_start: 0.8607 (mttm) cc_final: 0.8405 (mtpt) REVERT: A 238 GLN cc_start: 0.8654 (mt0) cc_final: 0.8412 (mt0) REVERT: A 270 MET cc_start: 0.8912 (mmm) cc_final: 0.8407 (mmm) REVERT: A 283 TRP cc_start: 0.7970 (OUTLIER) cc_final: 0.6499 (m-10) REVERT: B 91 MET cc_start: 0.9205 (mtm) cc_final: 0.8960 (mtm) REVERT: B 127 LYS cc_start: 0.8168 (tttt) cc_final: 0.7916 (tttm) REVERT: B 238 GLN cc_start: 0.8495 (mt0) cc_final: 0.8112 (mp10) REVERT: B 300 LYS cc_start: 0.6957 (mtmt) cc_final: 0.5551 (mmmt) REVERT: B 334 GLU cc_start: 0.5706 (OUTLIER) cc_final: 0.3995 (mt-10) REVERT: B 360 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8173 (p) REVERT: C 34 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8109 (mt-10) REVERT: C 99 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7110 (t0) REVERT: C 184 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: C 283 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7834 (m-10) REVERT: D 11 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8465 (tttm) REVERT: D 19 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7038 (pp20) REVERT: D 238 GLN cc_start: 0.8604 (mt0) cc_final: 0.8271 (mt0) REVERT: E 28 ASP cc_start: 0.8001 (m-30) cc_final: 0.7729 (m-30) REVERT: E 40 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5398 (mmt90) REVERT: E 71 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: E 154 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8606 (pt0) REVERT: E 161 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8193 (tp) REVERT: E 238 GLN cc_start: 0.8512 (mt0) cc_final: 0.8229 (mp10) REVERT: E 300 LYS cc_start: 0.8504 (tptt) cc_final: 0.8103 (mmmt) REVERT: E 321 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: E 326 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7200 (pp20) outliers start: 97 outliers final: 54 residues processed: 309 average time/residue: 1.2215 time to fit residues: 414.3866 Evaluate side-chains 300 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 91 MET 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 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 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 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 174 VAL Chi-restraints excluded: chain C residue 184 ASP 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 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 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 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 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 231 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 266 CYS Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 326 GLU 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 172 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 175 optimal weight: 0.0020 chunk 23 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- 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 ** 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 = 0.3458 r_free = 0.3458 target = 0.140737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.110512 restraints weight = 14581.953| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.75 r_work: 0.2864 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1872 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= 0.152 Angle : 0.621 7.525 19579 Z= 0.318 Chirality : 0.045 0.181 2186 Planarity : 0.005 0.048 2552 Dihedral : 8.008 67.966 1966 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 6.33 % Allowed : 23.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1786 helix: -0.94 (0.53), residues: 93 sheet: 0.28 (0.25), residues: 399 loop : -1.61 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 283 HIS 0.005 0.001 HIS B 282 PHE 0.015 0.002 PHE E 290 TYR 0.012 0.001 TYR D 223 ARG 0.003 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 368) hydrogen bonds : angle 5.21508 ( 1224) SS BOND : bond 0.00170 ( 5) SS BOND : angle 0.79298 ( 10) covalent geometry : bond 0.00374 (14351) covalent geometry : angle 0.62099 (19569) *********************** 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 326 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 226 time to evaluate : 1.713 Fit side-chains REVERT: A 11 LYS cc_start: 0.6655 (mmtt) cc_final: 0.5288 (tttp) REVERT: A 41 MET cc_start: 0.8184 (ptm) cc_final: 0.7148 (ptp) REVERT: A 183 LYS cc_start: 0.8400 (mttt) cc_final: 0.7848 (mtmt) REVERT: A 199 LYS cc_start: 0.8648 (mttm) cc_final: 0.8438 (mtpt) REVERT: A 238 GLN cc_start: 0.8835 (mt0) cc_final: 0.8612 (mt0) REVERT: A 270 MET cc_start: 0.9027 (mmm) cc_final: 0.8538 (mmm) REVERT: A 283 TRP cc_start: 0.8105 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: B 127 LYS cc_start: 0.8249 (tttt) cc_final: 0.7944 (tttm) REVERT: B 238 GLN cc_start: 0.8735 (mt0) cc_final: 0.8255 (mp10) REVERT: B 300 LYS cc_start: 0.7100 (mtmt) cc_final: 0.5575 (mmmt) REVERT: B 328 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: B 334 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.4195 (mt-10) REVERT: C 34 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: C 99 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.7140 (t0) REVERT: C 199 LYS cc_start: 0.8794 (mttm) cc_final: 0.8437 (mptt) REVERT: D 11 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8513 (tttm) REVERT: D 19 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7202 (pp20) REVERT: D 48 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7216 (mm-30) REVERT: D 161 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8372 (tt) REVERT: D 238 GLN cc_start: 0.8748 (mt0) cc_final: 0.8369 (mp10) REVERT: E 28 ASP cc_start: 0.8077 (m-30) cc_final: 0.7792 (m-30) REVERT: E 40 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.5948 (mmt-90) REVERT: E 71 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: E 154 GLU cc_start: 0.9140 (pt0) cc_final: 0.8790 (pt0) REVERT: E 161 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8180 (tp) REVERT: E 238 GLN cc_start: 0.8661 (mt0) cc_final: 0.8398 (mp10) REVERT: E 300 LYS cc_start: 0.8589 (tptt) cc_final: 0.8186 (mmmt) REVERT: E 321 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6469 (mp10) outliers start: 100 outliers final: 56 residues processed: 301 average time/residue: 1.2172 time to fit residues: 403.5875 Evaluate side-chains 290 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 223 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 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 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 108 SER 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 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 94 GLU Chi-restraints excluded: chain C residue 96 LEU 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 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 111 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 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 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 138 SER 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 321 GLN Chi-restraints excluded: chain E residue 350 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 139 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 103 optimal weight: 0.0270 chunk 10 optimal weight: 9.9990 chunk 158 optimal weight: 0.1980 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 226 ASN A 301 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** C 281 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.146307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116357 restraints weight = 14830.686| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.72 r_work: 0.2948 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14356 Z= 0.099 Angle : 0.546 6.700 19579 Z= 0.280 Chirality : 0.043 0.174 2186 Planarity : 0.005 0.039 2552 Dihedral : 7.158 61.178 1962 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.06 % Rotamer: Outliers : 5.51 % Allowed : 24.49 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.20), residues: 1786 helix: -0.88 (0.52), residues: 101 sheet: 0.32 (0.26), residues: 399 loop : -1.46 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.006 0.001 HIS B 282 PHE 0.011 0.001 PHE E 149 TYR 0.009 0.001 TYR A 289 ARG 0.002 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 368) hydrogen bonds : angle 4.75238 ( 1224) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.51875 ( 10) covalent geometry : bond 0.00239 (14351) covalent geometry : angle 0.54591 (19569) *********************** 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 337 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 250 time to evaluate : 1.553 Fit side-chains REVERT: A 11 LYS cc_start: 0.6631 (mmtt) cc_final: 0.5452 (tttm) REVERT: A 41 MET cc_start: 0.7934 (ptm) cc_final: 0.7218 (ptt) REVERT: A 125 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.8092 (t80) REVERT: A 183 LYS cc_start: 0.8315 (mttt) cc_final: 0.7867 (mtmt) REVERT: A 199 LYS cc_start: 0.8446 (mttm) cc_final: 0.8220 (mtpt) REVERT: A 238 GLN cc_start: 0.8608 (mt0) cc_final: 0.8304 (mt0) REVERT: A 270 MET cc_start: 0.8901 (mmm) cc_final: 0.8393 (mmm) REVERT: A 283 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6355 (m-10) REVERT: B 127 LYS cc_start: 0.8008 (tttt) cc_final: 0.7759 (ttmt) REVERT: B 130 ASP cc_start: 0.7645 (t70) cc_final: 0.6978 (t0) REVERT: B 133 ASN cc_start: 0.8280 (m-40) cc_final: 0.7825 (m110) REVERT: B 238 GLN cc_start: 0.8563 (mt0) cc_final: 0.8125 (mp10) REVERT: B 300 LYS cc_start: 0.6892 (mtmt) cc_final: 0.5468 (mmmt) REVERT: B 328 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6604 (pm20) REVERT: C 40 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7656 (tpp-160) REVERT: C 48 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7280 (mp0) REVERT: C 199 LYS cc_start: 0.8693 (mttm) cc_final: 0.8421 (mptt) REVERT: C 258 LYS cc_start: 0.7512 (ptpt) cc_final: 0.6506 (mmtp) REVERT: C 305 MET cc_start: 0.5014 (mmt) cc_final: 0.4560 (mpm) REVERT: D 11 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8479 (tttm) REVERT: D 48 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7146 (mm-30) REVERT: D 176 THR cc_start: 0.8557 (m) cc_final: 0.8082 (p) REVERT: D 238 GLN cc_start: 0.8531 (mt0) cc_final: 0.8178 (mp10) REVERT: E 28 ASP cc_start: 0.7940 (m-30) cc_final: 0.7662 (m-30) REVERT: E 40 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5625 (mmt90) REVERT: E 154 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: E 161 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8085 (tt) REVERT: E 238 GLN cc_start: 0.8437 (mt0) cc_final: 0.8200 (mp10) REVERT: E 250 GLU cc_start: 0.7691 (tt0) cc_final: 0.7349 (tt0) REVERT: E 305 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8133 (ptm) REVERT: E 361 LYS cc_start: 0.6412 (tmtt) cc_final: 0.6072 (tmtt) outliers start: 87 outliers final: 36 residues processed: 311 average time/residue: 1.1442 time to fit residues: 392.9995 Evaluate side-chains 273 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 229 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 125 PHE 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 108 SER 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 328 GLU 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 55 GLN 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 196 SER Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 283 TRP Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 111 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 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 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 266 CYS Chi-restraints excluded: chain E residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 69 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 141 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3458 r_free = 0.3458 target = 0.140096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.109072 restraints weight = 14866.709| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.78 r_work: 0.2844 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14356 Z= 0.198 Angle : 0.648 7.418 19579 Z= 0.333 Chirality : 0.047 0.213 2186 Planarity : 0.005 0.047 2552 Dihedral : 6.730 58.873 1942 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % Rotamer: Outliers : 6.01 % Allowed : 24.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1786 helix: -0.92 (0.52), residues: 101 sheet: 0.40 (0.25), residues: 401 loop : -1.46 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 283 HIS 0.004 0.001 HIS D 282 PHE 0.018 0.002 PHE E 290 TYR 0.016 0.002 TYR B 223 ARG 0.006 0.001 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 368) hydrogen bonds : angle 5.16146 ( 1224) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.78761 ( 10) covalent geometry : bond 0.00488 (14351) covalent geometry : angle 0.64817 (19569) *********************** 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 324 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 229 time to evaluate : 1.612 Fit side-chains REVERT: A 11 LYS cc_start: 0.6853 (mmtt) cc_final: 0.5436 (tttp) REVERT: A 41 MET cc_start: 0.8119 (ptm) cc_final: 0.7536 (ptm) REVERT: A 183 LYS cc_start: 0.8334 (mttt) cc_final: 0.7811 (mtmt) REVERT: A 238 GLN cc_start: 0.8914 (mt0) cc_final: 0.8700 (mt0) REVERT: A 270 MET cc_start: 0.9030 (mmm) cc_final: 0.8548 (mmm) REVERT: A 283 TRP cc_start: 0.8150 (OUTLIER) cc_final: 0.6691 (m-10) REVERT: A 300 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7701 (mtpt) REVERT: B 127 LYS cc_start: 0.8213 (tttt) cc_final: 0.7929 (ttmt) REVERT: B 130 ASP cc_start: 0.7802 (t70) cc_final: 0.7057 (t0) REVERT: B 133 ASN cc_start: 0.8232 (m-40) cc_final: 0.7713 (m110) REVERT: B 238 GLN cc_start: 0.8778 (mt0) cc_final: 0.8292 (mp10) REVERT: B 300 LYS cc_start: 0.7135 (mtmt) cc_final: 0.5584 (mmmt) REVERT: B 334 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.4103 (mt-10) REVERT: C 258 LYS cc_start: 0.7791 (ptpt) cc_final: 0.6615 (mmtt) REVERT: C 305 MET cc_start: 0.4931 (mmp) cc_final: 0.4629 (mpm) REVERT: C 326 GLU cc_start: 0.6850 (pm20) cc_final: 0.6627 (pm20) REVERT: D 11 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8499 (tttm) REVERT: D 161 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8435 (tt) REVERT: D 238 GLN cc_start: 0.8748 (mt0) cc_final: 0.8348 (mp10) REVERT: D 312 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8327 (tp) REVERT: E 28 ASP cc_start: 0.8044 (m-30) cc_final: 0.7764 (m-30) REVERT: E 40 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.5885 (mmt-90) REVERT: E 71 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6903 (mm-30) REVERT: E 154 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8797 (pt0) REVERT: E 161 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8303 (tp) REVERT: E 238 GLN cc_start: 0.8677 (mt0) cc_final: 0.8413 (mp10) REVERT: E 300 LYS cc_start: 0.8611 (tptt) cc_final: 0.8184 (mmmt) outliers start: 95 outliers final: 59 residues processed: 296 average time/residue: 1.2245 time to fit residues: 400.0225 Evaluate side-chains 291 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 223 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 192 LEU 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 300 LYS 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 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 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 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 91 MET 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 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 20 VAL Chi-restraints excluded: chain D residue 51 THR 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 84 MET 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 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 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 54 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 226 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 = 0.3477 r_free = 0.3477 target = 0.141995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.112070 restraints weight = 14869.605| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.73 r_work: 0.2874 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14356 Z= 0.137 Angle : 0.588 7.229 19579 Z= 0.303 Chirality : 0.044 0.190 2186 Planarity : 0.005 0.046 2552 Dihedral : 6.486 59.938 1942 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 5.25 % Allowed : 24.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1786 helix: -0.83 (0.53), residues: 101 sheet: 0.43 (0.25), residues: 401 loop : -1.40 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 283 HIS 0.004 0.001 HIS B 282 PHE 0.014 0.002 PHE E 290 TYR 0.012 0.001 TYR D 223 ARG 0.007 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.02806 ( 368) hydrogen bonds : angle 4.96745 ( 1224) SS BOND : bond 0.00173 ( 5) SS BOND : angle 1.02169 ( 10) covalent geometry : bond 0.00338 (14351) covalent geometry : angle 0.58818 (19569) *********************** 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 313 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 230 time to evaluate : 1.575 Fit side-chains REVERT: A 11 LYS cc_start: 0.6641 (mmtt) cc_final: 0.5458 (tttp) REVERT: A 41 MET cc_start: 0.7883 (ptm) cc_final: 0.7035 (ptt) REVERT: A 183 LYS cc_start: 0.8286 (mttt) cc_final: 0.7844 (mtmt) REVERT: A 238 GLN cc_start: 0.8698 (mt0) cc_final: 0.8481 (mt0) REVERT: A 270 MET cc_start: 0.8886 (mmm) cc_final: 0.8386 (mmm) REVERT: A 283 TRP cc_start: 0.7957 (OUTLIER) cc_final: 0.6512 (m-10) REVERT: A 316 MET cc_start: 0.2843 (mmm) cc_final: 0.2560 (mmm) REVERT: A 356 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7466 (mtt90) REVERT: B 41 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7439 (ttm) REVERT: B 130 ASP cc_start: 0.7781 (t70) cc_final: 0.7107 (t0) REVERT: B 133 ASN cc_start: 0.8333 (m-40) cc_final: 0.7794 (m110) REVERT: B 238 GLN cc_start: 0.8596 (mt0) cc_final: 0.8163 (mp10) REVERT: B 300 LYS cc_start: 0.6925 (mtmt) cc_final: 0.5523 (mmmt) REVERT: B 334 GLU cc_start: 0.5239 (OUTLIER) cc_final: 0.3946 (mt-10) REVERT: B 360 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8052 (p) REVERT: C 258 LYS cc_start: 0.7697 (ptpt) cc_final: 0.6542 (mmtp) REVERT: C 305 MET cc_start: 0.4885 (mmp) cc_final: 0.4533 (mpm) REVERT: C 326 GLU cc_start: 0.6744 (pm20) cc_final: 0.6524 (pm20) REVERT: D 11 LYS cc_start: 0.8890 (ttpt) cc_final: 0.8458 (tttm) REVERT: D 48 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7285 (mm-30) REVERT: D 161 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8269 (tt) REVERT: D 176 THR cc_start: 0.8641 (m) cc_final: 0.8150 (p) REVERT: D 238 GLN cc_start: 0.8537 (mt0) cc_final: 0.8170 (mp10) REVERT: D 312 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8264 (tp) REVERT: E 28 ASP cc_start: 0.7976 (m-30) cc_final: 0.7720 (m-30) REVERT: E 40 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5697 (mmt90) REVERT: E 154 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8580 (pt0) REVERT: E 161 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8123 (tp) REVERT: E 238 GLN cc_start: 0.8454 (mt0) cc_final: 0.8213 (mp10) REVERT: E 250 GLU cc_start: 0.7734 (tt0) cc_final: 0.7355 (tt0) outliers start: 83 outliers final: 54 residues processed: 290 average time/residue: 1.1699 time to fit residues: 372.9118 Evaluate side-chains 289 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 225 time to evaluate : 1.691 ------------------------------------------------------------------------------- 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 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 192 LEU 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 356 ARG Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 55 GLN 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 265 SER Chi-restraints excluded: chain B residue 280 VAL 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 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 55 GLN Chi-restraints excluded: chain C residue 91 MET 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 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 D residue 51 THR 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 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 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 266 CYS 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 147 optimal weight: 0.0670 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 226 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.140723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110402 restraints weight = 14726.171| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.75 r_work: 0.2852 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14356 Z= 0.167 Angle : 0.619 7.517 19579 Z= 0.318 Chirality : 0.045 0.215 2186 Planarity : 0.005 0.051 2552 Dihedral : 6.576 59.969 1942 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.61 % Favored : 92.27 % Rotamer: Outliers : 5.89 % Allowed : 24.05 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1786 helix: -0.87 (0.53), residues: 101 sheet: 0.46 (0.26), residues: 401 loop : -1.38 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 283 HIS 0.004 0.001 HIS D 282 PHE 0.015 0.002 PHE E 290 TYR 0.013 0.001 TYR D 223 ARG 0.007 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 368) hydrogen bonds : angle 5.06354 ( 1224) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.96929 ( 10) covalent geometry : bond 0.00414 (14351) covalent geometry : angle 0.61859 (19569) *********************** 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 319 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 226 time to evaluate : 1.765 Fit side-chains REVERT: A 11 LYS cc_start: 0.6646 (mmtt) cc_final: 0.5457 (tttm) REVERT: A 41 MET cc_start: 0.7864 (ptm) cc_final: 0.7325 (ptm) REVERT: A 64 ASN cc_start: 0.8680 (p0) cc_final: 0.8404 (p0) REVERT: A 183 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7862 (mtmt) REVERT: A 238 GLN cc_start: 0.8693 (mt0) cc_final: 0.8473 (mt0) REVERT: A 270 MET cc_start: 0.8891 (mmm) cc_final: 0.8387 (mmm) REVERT: A 283 TRP cc_start: 0.7970 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: A 300 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7648 (mtpt) REVERT: A 316 MET cc_start: 0.2571 (mmm) cc_final: 0.2281 (mmm) REVERT: B 41 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7471 (ttm) REVERT: B 130 ASP cc_start: 0.7803 (t70) cc_final: 0.7128 (t0) REVERT: B 133 ASN cc_start: 0.8379 (m-40) cc_final: 0.7803 (m110) REVERT: B 238 GLN cc_start: 0.8607 (mt0) cc_final: 0.8177 (mp10) REVERT: B 300 LYS cc_start: 0.6950 (mtmt) cc_final: 0.5517 (mmmt) REVERT: B 334 GLU cc_start: 0.5330 (OUTLIER) cc_final: 0.3991 (mt-10) REVERT: B 360 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8031 (p) REVERT: C 305 MET cc_start: 0.4897 (mmp) cc_final: 0.4577 (mpm) REVERT: C 326 GLU cc_start: 0.6815 (pm20) cc_final: 0.6586 (pm20) REVERT: D 11 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8454 (tttm) REVERT: D 48 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7324 (mm-30) REVERT: D 161 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8323 (tt) REVERT: D 176 THR cc_start: 0.8691 (m) cc_final: 0.8207 (p) REVERT: D 238 GLN cc_start: 0.8542 (mt0) cc_final: 0.8168 (mp10) REVERT: D 312 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8293 (tp) REVERT: E 28 ASP cc_start: 0.7963 (m-30) cc_final: 0.7710 (m-30) REVERT: E 40 ARG cc_start: 0.6461 (OUTLIER) cc_final: 0.5956 (mmt-90) REVERT: E 71 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6756 (mt-10) REVERT: E 154 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8595 (pt0) REVERT: E 161 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8153 (tp) REVERT: E 238 GLN cc_start: 0.8450 (mt0) cc_final: 0.8201 (mp10) REVERT: E 250 GLU cc_start: 0.7737 (tt0) cc_final: 0.7358 (tt0) REVERT: E 326 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7090 (pp20) outliers start: 93 outliers final: 61 residues processed: 291 average time/residue: 1.2388 time to fit residues: 396.0882 Evaluate side-chains 297 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 223 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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 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 192 LEU 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 317 LEU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 351 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 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 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 55 GLN Chi-restraints excluded: chain C residue 91 MET 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 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 1 LYS Chi-restraints excluded: chain D residue 51 THR 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 84 MET 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 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 273 ARG Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain E residue 356 ARG Chi-restraints excluded: chain E residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.141337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.111244 restraints weight = 14743.979| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.72 r_work: 0.2878 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14356 Z= 0.151 Angle : 0.604 7.756 19579 Z= 0.311 Chirality : 0.045 0.205 2186 Planarity : 0.005 0.059 2552 Dihedral : 6.486 59.515 1941 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 5.51 % Allowed : 24.37 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1786 helix: -0.84 (0.53), residues: 101 sheet: 0.45 (0.26), residues: 401 loop : -1.35 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 283 HIS 0.004 0.001 HIS D 282 PHE 0.014 0.002 PHE E 290 TYR 0.012 0.001 TYR D 223 ARG 0.007 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 368) hydrogen bonds : angle 5.00281 ( 1224) SS BOND : bond 0.00114 ( 5) SS BOND : angle 0.86323 ( 10) covalent geometry : bond 0.00372 (14351) covalent geometry : angle 0.60427 (19569) *********************** 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 311 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 224 time to evaluate : 1.555 Fit side-chains REVERT: A 11 LYS cc_start: 0.6830 (mmtt) cc_final: 0.5443 (tttp) REVERT: A 41 MET cc_start: 0.8043 (ptm) cc_final: 0.7479 (ptm) REVERT: A 64 ASN cc_start: 0.8659 (p0) cc_final: 0.8404 (p0) REVERT: A 183 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7831 (mtmt) REVERT: A 270 MET cc_start: 0.9007 (mmm) cc_final: 0.8477 (mmm) REVERT: A 283 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.6649 (m-10) REVERT: A 300 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7672 (mtpt) REVERT: A 316 MET cc_start: 0.2609 (mmm) cc_final: 0.2330 (mmm) REVERT: A 356 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7605 (mtt90) REVERT: B 41 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7708 (ttm) REVERT: B 130 ASP cc_start: 0.7791 (t70) cc_final: 0.7103 (t0) REVERT: B 133 ASN cc_start: 0.8402 (m-40) cc_final: 0.7745 (m110) REVERT: B 238 GLN cc_start: 0.8790 (mt0) cc_final: 0.8301 (mp10) REVERT: B 300 LYS cc_start: 0.7137 (mtmt) cc_final: 0.5589 (mmmt) REVERT: B 334 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.4046 (mt-10) REVERT: B 360 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8105 (p) REVERT: C 199 LYS cc_start: 0.8798 (mttp) cc_final: 0.8546 (mptt) REVERT: C 305 MET cc_start: 0.4947 (mmp) cc_final: 0.4618 (mpm) REVERT: D 11 LYS cc_start: 0.8986 (ttpt) cc_final: 0.8508 (tttm) REVERT: D 48 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7409 (mm-30) REVERT: D 130 ASP cc_start: 0.7479 (t0) cc_final: 0.6879 (t0) REVERT: D 161 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8377 (tt) REVERT: D 176 THR cc_start: 0.8634 (m) cc_final: 0.8138 (p) REVERT: D 238 GLN cc_start: 0.8714 (mt0) cc_final: 0.8334 (mp10) REVERT: D 312 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8314 (tp) REVERT: E 28 ASP cc_start: 0.8005 (m-30) cc_final: 0.7761 (m-30) REVERT: E 40 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.5933 (mmt-90) REVERT: E 71 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6893 (mt-10) REVERT: E 154 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8770 (pt0) REVERT: E 161 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8174 (tp) REVERT: E 238 GLN cc_start: 0.8701 (mt0) cc_final: 0.8425 (mp10) REVERT: E 250 GLU cc_start: 0.7839 (tt0) cc_final: 0.7480 (tt0) REVERT: E 326 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7256 (pp20) outliers start: 87 outliers final: 59 residues processed: 283 average time/residue: 1.1787 time to fit residues: 365.6972 Evaluate side-chains 293 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 220 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 96 LEU 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 172 GLU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 192 LEU 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 351 THR Chi-restraints excluded: chain A residue 356 ARG 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 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 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 55 GLN 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 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 D residue 1 LYS 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 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 84 MET 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 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 273 ARG Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 326 GLU 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 143 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 114 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 315 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 = 0.3492 r_free = 0.3492 target = 0.143331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.113333 restraints weight = 14819.436| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.73 r_work: 0.2892 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14356 Z= 0.120 Angle : 0.572 7.333 19579 Z= 0.295 Chirality : 0.043 0.187 2186 Planarity : 0.005 0.062 2552 Dihedral : 6.307 58.760 1941 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.55 % Rotamer: Outliers : 4.94 % Allowed : 25.06 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1786 helix: -0.75 (0.53), residues: 101 sheet: 0.48 (0.26), residues: 394 loop : -1.29 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.004 0.001 HIS D 282 PHE 0.012 0.002 PHE E 290 TYR 0.011 0.001 TYR D 223 ARG 0.005 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 368) hydrogen bonds : angle 4.84363 ( 1224) SS BOND : bond 0.00123 ( 5) SS BOND : angle 0.73277 ( 10) covalent geometry : bond 0.00294 (14351) covalent geometry : angle 0.57157 (19569) ********************** 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 307 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 229 time to evaluate : 1.724 Fit side-chains REVERT: A 11 LYS cc_start: 0.6582 (mmtt) cc_final: 0.5427 (tttp) REVERT: A 41 MET cc_start: 0.7782 (ptm) cc_final: 0.6927 (ptt) REVERT: A 64 ASN cc_start: 0.8603 (p0) cc_final: 0.8332 (p0) REVERT: A 183 LYS cc_start: 0.8266 (mttt) cc_final: 0.7814 (mtmt) REVERT: A 270 MET cc_start: 0.8880 (mmm) cc_final: 0.8328 (mmm) REVERT: A 283 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.6489 (m-10) REVERT: A 316 MET cc_start: 0.2813 (mmm) cc_final: 0.2510 (mmm) REVERT: A 356 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7502 (mtt90) REVERT: B 41 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7436 (ttm) REVERT: B 130 ASP cc_start: 0.7768 (t70) cc_final: 0.7169 (t0) REVERT: B 133 ASN cc_start: 0.8417 (m-40) cc_final: 0.7812 (m110) REVERT: B 238 GLN cc_start: 0.8589 (mt0) cc_final: 0.8125 (mp10) REVERT: B 300 LYS cc_start: 0.6934 (mtmt) cc_final: 0.5506 (mmmt) REVERT: B 360 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8110 (p) REVERT: C 40 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7817 (mmt90) REVERT: C 199 LYS cc_start: 0.8660 (mttp) cc_final: 0.8442 (mptt) REVERT: C 258 LYS cc_start: 0.7784 (ptpp) cc_final: 0.7397 (ptpt) REVERT: C 305 MET cc_start: 0.4877 (mmp) cc_final: 0.4533 (mpm) REVERT: C 316 MET cc_start: 0.5007 (mmt) cc_final: 0.4119 (mmm) REVERT: D 11 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8458 (tttm) REVERT: D 48 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7326 (mm-30) REVERT: D 176 THR cc_start: 0.8616 (m) cc_final: 0.8104 (p) REVERT: D 238 GLN cc_start: 0.8520 (mt0) cc_final: 0.8170 (mp10) REVERT: D 312 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8309 (tt) REVERT: E 28 ASP cc_start: 0.7890 (m-30) cc_final: 0.7654 (m-30) REVERT: E 40 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.5696 (mmt90) REVERT: E 71 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6794 (mt-10) REVERT: E 154 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8554 (pt0) REVERT: E 161 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8107 (tp) REVERT: E 238 GLN cc_start: 0.8444 (mt0) cc_final: 0.8194 (mp10) REVERT: E 250 GLU cc_start: 0.7682 (tt0) cc_final: 0.7203 (tt0) REVERT: E 326 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7070 (pp20) outliers start: 78 outliers final: 53 residues processed: 285 average time/residue: 1.2279 time to fit residues: 387.1205 Evaluate side-chains 288 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 96 LEU 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 192 LEU 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 356 ARG 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 221 THR Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 330 THR 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 55 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 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 315 ASN Chi-restraints excluded: chain D residue 1 LYS Chi-restraints excluded: chain D residue 51 THR 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 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 84 MET 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 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 305 MET Chi-restraints excluded: chain E residue 326 GLU 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 156 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 176 optimal weight: 0.0020 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- 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 64 ASN B 226 ASN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.143109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.113149 restraints weight = 14908.979| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.73 r_work: 0.2904 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 14356 Z= 0.175 Angle : 0.847 59.200 19579 Z= 0.493 Chirality : 0.048 0.897 2186 Planarity : 0.006 0.155 2552 Dihedral : 6.313 58.741 1941 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.50 % Rotamer: Outliers : 4.24 % Allowed : 25.89 % Favored : 69.87 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.20), residues: 1786 helix: -0.76 (0.54), residues: 101 sheet: 0.49 (0.26), residues: 394 loop : -1.29 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.004 0.001 HIS D 282 PHE 0.012 0.002 PHE E 290 TYR 0.011 0.001 TYR D 223 ARG 0.004 0.000 ARG B 276 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 368) hydrogen bonds : angle 4.84619 ( 1224) SS BOND : bond 0.00120 ( 5) SS BOND : angle 0.70429 ( 10) covalent geometry : bond 0.00381 (14351) covalent geometry : angle 0.84682 (19569) =============================================================================== Job complete usr+sys time: 11614.36 seconds wall clock time: 197 minutes 55.20 seconds (11875.20 seconds total)