Starting phenix.real_space_refine on Thu Sep 26 16:50:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/09_2024/7k25_22643.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/09_2024/7k25_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/09_2024/7k25_22643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/09_2024/7k25_22643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/09_2024/7k25_22643.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k25_22643/09_2024/7k25_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-5461/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: 8.51, per 1000 atoms: 0.61 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: 2.90 Conformation dependent library (CDL) restraints added in 1.7 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: 1.85 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: 5.69 Time building geometry restraints manager: 3.52 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: 2.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.600 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.500 ------------------------------------------------------------------------------- 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 14351 Z= 0.599 Angle : 0.942 10.241 19569 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 *********************** 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 fitting. rotamer outliers: 145 poor density : 275 time to evaluate : 1.441 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: 1.1362 time to fit residues: 479.3289 Evaluate side-chains 341 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 245 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14351 Z= 0.195 Angle : 0.611 8.216 19569 Z= 0.318 Chirality : 0.044 0.160 2186 Planarity : 0.006 0.054 2552 Dihedral : 9.903 70.019 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 : 22.53 % Favored : 71.77 % 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 *********************** 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 fitting. rotamer outliers: 90 poor density : 267 time to evaluate : 1.713 Fit side-chains REVERT: A 11 LYS cc_start: 0.6192 (mmtt) cc_final: 0.5567 (tttm) REVERT: A 41 MET cc_start: 0.7734 (ptm) cc_final: 0.7174 (ptp) REVERT: A 183 LYS cc_start: 0.8287 (mttt) cc_final: 0.8026 (mtmt) REVERT: A 199 LYS cc_start: 0.8377 (mttm) cc_final: 0.8165 (mtpt) REVERT: A 238 GLN cc_start: 0.8042 (mt0) cc_final: 0.7787 (mt0) REVERT: A 249 ASP cc_start: 0.8449 (p0) cc_final: 0.8209 (p0) REVERT: A 283 TRP cc_start: 0.7782 (OUTLIER) cc_final: 0.6280 (m-10) REVERT: A 300 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7849 (mtpt) REVERT: B 91 MET cc_start: 0.8879 (mtm) cc_final: 0.8565 (mtm) REVERT: B 127 LYS cc_start: 0.8063 (tttt) cc_final: 0.7837 (tttm) REVERT: B 183 LYS cc_start: 0.8618 (mptt) cc_final: 0.8269 (mptp) REVERT: B 238 GLN cc_start: 0.7908 (mt0) cc_final: 0.7690 (mp10) REVERT: B 300 LYS cc_start: 0.6745 (mtmt) cc_final: 0.5828 (mmmt) REVERT: B 334 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.3939 (mt-10) REVERT: C 99 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6996 (t0) REVERT: C 199 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8282 (mptt) REVERT: D 11 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8515 (tttm) REVERT: D 19 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6817 (pp20) REVERT: E 20 VAL cc_start: 0.8514 (t) cc_final: 0.8179 (m) REVERT: E 28 ASP cc_start: 0.7541 (m-30) cc_final: 0.7341 (m-30) REVERT: E 40 ARG cc_start: 0.5973 (mtm180) cc_final: 0.5314 (mmt90) REVERT: E 154 GLU cc_start: 0.8490 (pt0) cc_final: 0.8125 (pt0) REVERT: E 161 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.7998 (tp) REVERT: E 238 GLN cc_start: 0.7970 (mt0) cc_final: 0.7730 (mp10) REVERT: E 321 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6242 (mp10) REVERT: E 361 LYS cc_start: 0.6101 (tmtt) cc_final: 0.5676 (tmtt) outliers start: 90 outliers final: 33 residues processed: 333 average time/residue: 1.1884 time to fit residues: 434.7363 Evaluate side-chains 274 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 233 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 89 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 133 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 102 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14351 Z= 0.379 Angle : 0.714 8.255 19569 Z= 0.366 Chirality : 0.049 0.204 2186 Planarity : 0.006 0.054 2552 Dihedral : 8.651 69.294 1966 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.94 % Rotamer: Outliers : 6.20 % Allowed : 23.67 % 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: -1.91 (0.19), residues: 1786 helix: -1.69 (0.47), residues: 106 sheet: 0.12 (0.25), residues: 398 loop : -1.83 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 283 HIS 0.004 0.001 HIS D 281 PHE 0.021 0.002 PHE B 290 TYR 0.016 0.002 TYR D 223 ARG 0.006 0.001 ARG C 40 *********************** 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 334 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 236 time to evaluate : 1.513 Fit side-chains REVERT: A 11 LYS cc_start: 0.6394 (mmtt) cc_final: 0.5690 (tttm) REVERT: A 41 MET cc_start: 0.7822 (ptm) cc_final: 0.6975 (ptp) REVERT: A 183 LYS cc_start: 0.8336 (mttt) cc_final: 0.8042 (mtmt) REVERT: A 238 GLN cc_start: 0.8193 (mt0) cc_final: 0.7795 (tt0) REVERT: A 270 MET cc_start: 0.8641 (mmm) cc_final: 0.8107 (mmm) REVERT: A 283 TRP cc_start: 0.7884 (OUTLIER) cc_final: 0.6525 (m-10) REVERT: B 91 MET cc_start: 0.8874 (mtm) cc_final: 0.8573 (mtm) REVERT: B 127 LYS cc_start: 0.8101 (tttt) cc_final: 0.7887 (tttm) REVERT: B 300 LYS cc_start: 0.6721 (mtmt) cc_final: 0.5768 (mmmt) REVERT: B 334 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.3934 (mt-10) REVERT: B 360 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8214 (p) REVERT: C 34 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7865 (mt-10) REVERT: C 99 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7054 (t0) REVERT: C 184 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: C 283 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7728 (m-90) REVERT: D 11 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8494 (tttm) REVERT: D 19 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6832 (pp20) REVERT: D 161 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8365 (tt) REVERT: D 238 GLN cc_start: 0.8060 (mt0) cc_final: 0.7728 (mt0) REVERT: E 40 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5485 (mmt90) REVERT: E 71 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6730 (mm-30) REVERT: E 154 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: E 161 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8214 (tp) REVERT: E 238 GLN cc_start: 0.7984 (mt0) cc_final: 0.7743 (mt0) REVERT: E 300 LYS cc_start: 0.8329 (tptt) cc_final: 0.7953 (mmmt) REVERT: E 321 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6550 (mp10) outliers start: 98 outliers final: 55 residues processed: 307 average time/residue: 1.1322 time to fit residues: 383.0119 Evaluate side-chains 298 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 229 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 195 ILE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 221 THR 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 C residue 344 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 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 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 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 159 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 108 optimal weight: 0.0060 chunk 161 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14351 Z= 0.295 Angle : 0.655 8.115 19569 Z= 0.336 Chirality : 0.046 0.205 2186 Planarity : 0.006 0.050 2552 Dihedral : 8.343 69.960 1966 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 6.71 % Allowed : 24.11 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.19), residues: 1786 helix: -1.29 (0.50), residues: 100 sheet: 0.29 (0.25), residues: 396 loop : -1.68 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 283 HIS 0.005 0.001 HIS B 282 PHE 0.017 0.002 PHE E 290 TYR 0.012 0.001 TYR D 223 ARG 0.003 0.000 ARG C 40 *********************** 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 334 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 228 time to evaluate : 1.719 Fit side-chains REVERT: A 11 LYS cc_start: 0.6174 (mmtt) cc_final: 0.5564 (tttm) REVERT: A 41 MET cc_start: 0.7770 (ptm) cc_final: 0.6954 (ptp) REVERT: A 183 LYS cc_start: 0.8312 (mttt) cc_final: 0.8016 (mtmt) REVERT: A 238 GLN cc_start: 0.8105 (mt0) cc_final: 0.7850 (mt0) REVERT: A 267 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8754 (p) REVERT: A 270 MET cc_start: 0.8638 (mmm) cc_final: 0.8109 (mmm) REVERT: A 283 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.6435 (m-10) REVERT: B 91 MET cc_start: 0.8868 (mtm) cc_final: 0.8639 (mtm) REVERT: B 127 LYS cc_start: 0.8041 (tttt) cc_final: 0.7834 (tttm) REVERT: B 300 LYS cc_start: 0.6754 (mtmt) cc_final: 0.5787 (mmmt) REVERT: B 328 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6269 (pm20) REVERT: B 334 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.4154 (mt-10) REVERT: C 34 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: C 99 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6993 (t0) REVERT: C 185 MET cc_start: 0.8555 (mtm) cc_final: 0.8338 (mtm) REVERT: D 11 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8498 (tttm) REVERT: D 19 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6871 (pp20) REVERT: D 238 GLN cc_start: 0.7997 (mt0) cc_final: 0.7701 (mp10) REVERT: E 40 ARG cc_start: 0.6254 (OUTLIER) cc_final: 0.5708 (mmt90) REVERT: E 71 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6689 (mm-30) REVERT: E 154 GLU cc_start: 0.8532 (pt0) cc_final: 0.8176 (pt0) REVERT: E 161 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8113 (tp) REVERT: E 238 GLN cc_start: 0.7952 (mt0) cc_final: 0.7745 (mp10) REVERT: E 300 LYS cc_start: 0.8336 (tptt) cc_final: 0.7951 (mmmt) REVERT: E 321 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6229 (mp10) REVERT: E 326 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6716 (pp20) outliers start: 106 outliers final: 62 residues processed: 304 average time/residue: 1.1368 time to fit residues: 380.6773 Evaluate side-chains 297 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 223 time to evaluate : 1.585 ------------------------------------------------------------------------------- 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 218 ASN Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 283 TRP Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 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 C residue 344 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 138 SER 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 266 CYS Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 321 GLN Chi-restraints excluded: chain E residue 326 GLU 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 142 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 301 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14351 Z= 0.231 Angle : 0.612 7.737 19569 Z= 0.313 Chirality : 0.045 0.183 2186 Planarity : 0.005 0.048 2552 Dihedral : 7.865 67.813 1963 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 91.99 % Rotamer: Outliers : 6.27 % Allowed : 24.43 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.19), residues: 1786 helix: -0.81 (0.54), residues: 93 sheet: 0.30 (0.26), residues: 401 loop : -1.51 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 283 HIS 0.005 0.001 HIS B 282 PHE 0.014 0.002 PHE E 290 TYR 0.012 0.001 TYR D 223 ARG 0.004 0.000 ARG B 276 *********************** 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 335 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 236 time to evaluate : 1.640 Fit side-chains REVERT: A 11 LYS cc_start: 0.6186 (mmtt) cc_final: 0.5578 (tttm) REVERT: A 41 MET cc_start: 0.7717 (ptm) cc_final: 0.6891 (ptp) REVERT: A 183 LYS cc_start: 0.8282 (mttt) cc_final: 0.8007 (mtmt) REVERT: A 238 GLN cc_start: 0.8065 (mt0) cc_final: 0.7778 (mt0) REVERT: A 267 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 270 MET cc_start: 0.8637 (mmm) cc_final: 0.8131 (mmm) REVERT: A 283 TRP cc_start: 0.7851 (OUTLIER) cc_final: 0.6422 (m-10) REVERT: A 300 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: B 41 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7658 (mmm) REVERT: B 91 MET cc_start: 0.8864 (mtm) cc_final: 0.8657 (mtm) REVERT: B 127 LYS cc_start: 0.8048 (tttt) cc_final: 0.7765 (tttm) REVERT: B 300 LYS cc_start: 0.6747 (mtmt) cc_final: 0.5792 (mmmt) REVERT: B 328 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: B 334 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.4124 (mt-10) REVERT: C 34 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: C 99 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6905 (t0) REVERT: C 185 MET cc_start: 0.8611 (mtm) cc_final: 0.8306 (mtm) REVERT: C 258 LYS cc_start: 0.7815 (ptpt) cc_final: 0.6874 (mmtt) REVERT: C 295 ARG cc_start: 0.8713 (ptt180) cc_final: 0.8469 (ptt180) REVERT: D 11 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8501 (tttm) REVERT: D 19 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6941 (pp20) REVERT: D 48 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7139 (mm-30) REVERT: D 238 GLN cc_start: 0.7962 (mt0) cc_final: 0.7681 (mp10) REVERT: E 71 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6604 (mm-30) REVERT: E 154 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: E 161 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8054 (tp) REVERT: E 300 LYS cc_start: 0.8311 (tptt) cc_final: 0.7943 (mmmt) REVERT: E 305 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8024 (ptm) REVERT: E 321 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6346 (mp10) REVERT: E 326 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6763 (pp20) outliers start: 99 outliers final: 54 residues processed: 304 average time/residue: 1.1593 time to fit residues: 388.9167 Evaluate side-chains 294 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 225 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 267 VAL 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 344 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 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 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 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 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 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 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 356 ARG Chi-restraints excluded: chain E residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 218 ASN B 238 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14351 Z= 0.222 Angle : 0.596 6.999 19569 Z= 0.306 Chirality : 0.044 0.176 2186 Planarity : 0.005 0.045 2552 Dihedral : 7.581 65.446 1960 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 6.39 % Allowed : 23.99 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.20), residues: 1786 helix: -0.94 (0.52), residues: 101 sheet: 0.37 (0.26), residues: 402 loop : -1.44 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 0.005 0.000 ARG E 40 *********************** 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 336 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 235 time to evaluate : 1.523 Fit side-chains REVERT: A 11 LYS cc_start: 0.6392 (mmtt) cc_final: 0.5717 (tttm) REVERT: A 41 MET cc_start: 0.7640 (ptm) cc_final: 0.7136 (ptm) REVERT: A 64 ASN cc_start: 0.8661 (p0) cc_final: 0.8328 (p0) REVERT: A 183 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7987 (mtmt) REVERT: A 199 LYS cc_start: 0.8341 (mtpt) cc_final: 0.8124 (mmtt) REVERT: A 238 GLN cc_start: 0.8113 (mt0) cc_final: 0.7826 (mt0) REVERT: A 267 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8732 (p) REVERT: A 270 MET cc_start: 0.8625 (mmm) cc_final: 0.8139 (mmm) REVERT: A 283 TRP cc_start: 0.7837 (OUTLIER) cc_final: 0.6428 (m-10) REVERT: A 300 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7901 (mtpt) REVERT: B 91 MET cc_start: 0.8862 (mtm) cc_final: 0.8654 (mtm) REVERT: B 127 LYS cc_start: 0.8036 (tttt) cc_final: 0.7757 (ttmt) REVERT: B 130 ASP cc_start: 0.7743 (t70) cc_final: 0.7272 (t0) REVERT: B 300 LYS cc_start: 0.6759 (mtmt) cc_final: 0.5788 (mmmt) REVERT: B 334 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4145 (mt-10) REVERT: C 34 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: C 185 MET cc_start: 0.8716 (mtm) cc_final: 0.8386 (mtm) REVERT: C 258 LYS cc_start: 0.7603 (ptpt) cc_final: 0.6946 (mmtp) REVERT: C 295 ARG cc_start: 0.8706 (ptt180) cc_final: 0.8441 (ptt180) REVERT: D 11 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8499 (tttm) REVERT: D 48 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7217 (mm-30) REVERT: D 176 THR cc_start: 0.8670 (m) cc_final: 0.8191 (p) REVERT: D 238 GLN cc_start: 0.7941 (mt0) cc_final: 0.7678 (mp10) REVERT: D 312 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8307 (tp) REVERT: E 71 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6524 (mm-30) REVERT: E 154 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: E 161 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8062 (tp) REVERT: E 250 GLU cc_start: 0.7332 (tt0) cc_final: 0.6992 (tt0) REVERT: E 300 LYS cc_start: 0.8329 (tptt) cc_final: 0.7950 (mmmt) REVERT: E 305 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.8048 (ptm) REVERT: E 321 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6330 (mp10) outliers start: 101 outliers final: 58 residues processed: 308 average time/residue: 1.1489 time to fit residues: 389.8471 Evaluate side-chains 292 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 222 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL 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 344 VAL Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 341 THR 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 40 ARG Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 102 GLN Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 154 GLU 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 51 THR Chi-restraints excluded: chain D residue 111 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 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 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 305 MET Chi-restraints excluded: chain E residue 321 GLN 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 165 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 238 GLN D 55 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14351 Z= 0.184 Angle : 0.567 6.581 19569 Z= 0.291 Chirality : 0.043 0.164 2186 Planarity : 0.005 0.041 2552 Dihedral : 7.156 62.410 1956 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.50 % Rotamer: Outliers : 5.38 % Allowed : 25.25 % Favored : 69.37 % 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: 0.38 (0.26), residues: 392 loop : -1.36 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.004 0.001 HIS B 282 PHE 0.011 0.001 PHE E 290 TYR 0.010 0.001 TYR D 223 ARG 0.003 0.000 ARG E 40 *********************** 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 317 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 232 time to evaluate : 1.592 Fit side-chains REVERT: A 11 LYS cc_start: 0.6376 (mmtt) cc_final: 0.5718 (tttm) REVERT: A 41 MET cc_start: 0.7564 (ptm) cc_final: 0.6832 (ptt) REVERT: A 64 ASN cc_start: 0.8597 (p0) cc_final: 0.8286 (p0) REVERT: A 172 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: A 183 LYS cc_start: 0.8222 (mttt) cc_final: 0.7956 (mtmt) REVERT: A 199 LYS cc_start: 0.8321 (mtpt) cc_final: 0.8068 (mmtt) REVERT: A 238 GLN cc_start: 0.8066 (mt0) cc_final: 0.7780 (mt0) REVERT: A 267 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8724 (p) REVERT: A 270 MET cc_start: 0.8607 (mmm) cc_final: 0.8046 (mmm) REVERT: A 283 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.6355 (m-10) REVERT: A 300 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7787 (mtpt) REVERT: A 356 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7434 (mtt90) REVERT: B 41 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7582 (mmm) REVERT: B 91 MET cc_start: 0.8855 (mtm) cc_final: 0.8636 (mtm) REVERT: B 127 LYS cc_start: 0.7981 (tttt) cc_final: 0.7675 (ttmt) REVERT: B 130 ASP cc_start: 0.7722 (t70) cc_final: 0.7263 (t0) REVERT: B 300 LYS cc_start: 0.6752 (mtmt) cc_final: 0.5784 (mmmt) REVERT: B 334 GLU cc_start: 0.5175 (OUTLIER) cc_final: 0.3986 (mt-10) REVERT: C 185 MET cc_start: 0.8735 (mtm) cc_final: 0.8390 (mtm) REVERT: C 199 LYS cc_start: 0.8423 (mptt) cc_final: 0.8209 (tppt) REVERT: C 258 LYS cc_start: 0.7512 (ptpt) cc_final: 0.6832 (mmtp) REVERT: C 295 ARG cc_start: 0.8667 (ptt180) cc_final: 0.8400 (ptt180) REVERT: D 11 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8502 (tttm) REVERT: D 48 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7201 (mm-30) REVERT: D 176 THR cc_start: 0.8636 (m) cc_final: 0.8147 (p) REVERT: D 238 GLN cc_start: 0.7925 (mt0) cc_final: 0.7673 (mp10) REVERT: D 312 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8307 (tt) REVERT: E 154 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8102 (pt0) REVERT: E 161 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8060 (tp) REVERT: E 250 GLU cc_start: 0.7302 (tt0) cc_final: 0.6951 (tt0) REVERT: E 305 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8046 (ptm) outliers start: 85 outliers final: 51 residues processed: 295 average time/residue: 1.2050 time to fit residues: 390.9407 Evaluate side-chains 286 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 224 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL 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 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 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 280 VAL Chi-restraints excluded: chain B residue 330 THR 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 40 ARG Chi-restraints excluded: chain C residue 55 GLN 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 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 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 46 THR 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 305 MET Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 B 238 GLN D 55 GLN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14351 Z= 0.239 Angle : 0.600 6.809 19569 Z= 0.308 Chirality : 0.044 0.203 2186 Planarity : 0.005 0.063 2552 Dihedral : 6.891 61.647 1949 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.22 % Favored : 92.72 % Rotamer: Outliers : 5.32 % Allowed : 25.38 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.20), residues: 1786 helix: -0.82 (0.53), residues: 101 sheet: 0.43 (0.26), residues: 402 loop : -1.35 (0.17), residues: 1283 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 0.013 0.001 TYR D 223 ARG 0.003 0.000 ARG E 40 *********************** 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 308 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 224 time to evaluate : 1.688 Fit side-chains REVERT: A 11 LYS cc_start: 0.6345 (mmtt) cc_final: 0.5687 (tttm) REVERT: A 41 MET cc_start: 0.7554 (ptm) cc_final: 0.7072 (ptm) REVERT: A 64 ASN cc_start: 0.8657 (p0) cc_final: 0.8349 (p0) REVERT: A 183 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7945 (mtmt) REVERT: A 199 LYS cc_start: 0.8302 (mtpt) cc_final: 0.8095 (mmtt) REVERT: A 238 GLN cc_start: 0.8163 (mt0) cc_final: 0.7904 (mt0) REVERT: A 267 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 270 MET cc_start: 0.8633 (mmm) cc_final: 0.8144 (mmm) REVERT: A 283 TRP cc_start: 0.7829 (OUTLIER) cc_final: 0.6453 (m-10) REVERT: A 300 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7786 (mtpt) REVERT: A 316 MET cc_start: 0.2898 (mmm) cc_final: 0.2683 (mmm) REVERT: B 41 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7501 (mmm) REVERT: B 91 MET cc_start: 0.8850 (mtm) cc_final: 0.8635 (mtm) REVERT: B 127 LYS cc_start: 0.7996 (tttt) cc_final: 0.7690 (ttmt) REVERT: B 130 ASP cc_start: 0.7797 (t70) cc_final: 0.7300 (t0) REVERT: B 300 LYS cc_start: 0.6768 (mtmt) cc_final: 0.5791 (mmmt) REVERT: B 334 GLU cc_start: 0.5384 (OUTLIER) cc_final: 0.4044 (mt-10) REVERT: C 94 GLU cc_start: 0.3439 (OUTLIER) cc_final: 0.3229 (mt-10) REVERT: C 185 MET cc_start: 0.8741 (mtm) cc_final: 0.8330 (mtm) REVERT: C 199 LYS cc_start: 0.8456 (mptt) cc_final: 0.8058 (mmtt) REVERT: C 258 LYS cc_start: 0.7575 (ptpt) cc_final: 0.6909 (mmtp) REVERT: C 295 ARG cc_start: 0.8701 (ptt180) cc_final: 0.8418 (ptt180) REVERT: D 11 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8500 (tttm) REVERT: D 48 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7198 (mm-30) REVERT: D 238 GLN cc_start: 0.7927 (mt0) cc_final: 0.7658 (mp10) REVERT: E 71 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: E 154 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: E 161 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8072 (tp) REVERT: E 250 GLU cc_start: 0.7319 (tt0) cc_final: 0.6960 (tt0) REVERT: E 305 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8054 (ptm) REVERT: E 326 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6967 (pp20) outliers start: 84 outliers final: 58 residues processed: 284 average time/residue: 1.2008 time to fit residues: 378.1479 Evaluate side-chains 292 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 222 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 172 GLU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL 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 350 MET Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 273 ARG 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 350 MET 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 94 GLU 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 154 GLU 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 20 VAL Chi-restraints excluded: chain D residue 51 THR 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 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 116 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 266 CYS 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 350 MET 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 163 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 0.0370 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.0980 chunk 143 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 104 optimal weight: 0.4980 chunk 168 optimal weight: 2.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- 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 B 238 GLN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14351 Z= 0.189 Angle : 0.567 6.458 19569 Z= 0.292 Chirality : 0.043 0.188 2186 Planarity : 0.005 0.061 2552 Dihedral : 6.603 59.866 1949 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.67 % Rotamer: Outliers : 4.62 % Allowed : 25.82 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.20), residues: 1786 helix: -0.96 (0.50), residues: 109 sheet: 0.44 (0.26), residues: 393 loop : -1.28 (0.17), residues: 1284 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 0.011 0.002 PHE E 290 TYR 0.010 0.001 TYR D 223 ARG 0.003 0.000 ARG E 40 *********************** 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 304 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 231 time to evaluate : 1.560 Fit side-chains REVERT: A 11 LYS cc_start: 0.6331 (mmtt) cc_final: 0.5685 (tttm) REVERT: A 41 MET cc_start: 0.7536 (ptm) cc_final: 0.6801 (ptt) REVERT: A 64 ASN cc_start: 0.8601 (p0) cc_final: 0.8340 (p0) REVERT: A 183 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: A 199 LYS cc_start: 0.8254 (mtpt) cc_final: 0.8044 (mmtt) REVERT: A 238 GLN cc_start: 0.8069 (mt0) cc_final: 0.7783 (mt0) REVERT: A 267 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8713 (p) REVERT: A 270 MET cc_start: 0.8621 (mmm) cc_final: 0.8063 (mmm) REVERT: A 283 TRP cc_start: 0.7740 (OUTLIER) cc_final: 0.6374 (m-10) REVERT: A 316 MET cc_start: 0.2813 (mmm) cc_final: 0.2540 (mmm) REVERT: A 356 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7371 (mtt90) REVERT: B 91 MET cc_start: 0.8843 (mtm) cc_final: 0.8625 (mtm) REVERT: B 127 LYS cc_start: 0.8028 (tttt) cc_final: 0.7740 (ttmt) REVERT: B 130 ASP cc_start: 0.7778 (t70) cc_final: 0.7329 (t0) REVERT: B 300 LYS cc_start: 0.6746 (mtmt) cc_final: 0.5772 (mmmt) REVERT: C 40 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7869 (mmt90) REVERT: C 185 MET cc_start: 0.8799 (mtm) cc_final: 0.8294 (mtm) REVERT: C 258 LYS cc_start: 0.7475 (ptpt) cc_final: 0.6708 (mmtp) REVERT: C 295 ARG cc_start: 0.8659 (ptt180) cc_final: 0.8371 (ptt180) REVERT: D 11 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8498 (tttm) REVERT: D 48 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 176 THR cc_start: 0.8602 (m) cc_final: 0.8077 (p) REVERT: D 238 GLN cc_start: 0.7924 (mt0) cc_final: 0.7668 (mp10) REVERT: E 154 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: E 161 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8060 (tp) REVERT: E 250 GLU cc_start: 0.7310 (tt0) cc_final: 0.6956 (tt0) REVERT: E 305 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.8044 (ptm) REVERT: E 326 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6967 (pp20) outliers start: 73 outliers final: 52 residues processed: 278 average time/residue: 1.1324 time to fit residues: 346.9153 Evaluate side-chains 284 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 223 time to evaluate : 1.568 ------------------------------------------------------------------------------- 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 183 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL 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 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 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 280 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 341 THR 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 40 ARG Chi-restraints excluded: chain C residue 55 GLN 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 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 208 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 THR 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 305 MET Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain E residue 350 MET Chi-restraints excluded: chain E residue 356 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 B 238 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 GLN D 77 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14351 Z= 0.218 Angle : 0.583 6.978 19569 Z= 0.300 Chirality : 0.044 0.192 2186 Planarity : 0.005 0.063 2552 Dihedral : 6.403 56.482 1944 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.78 % Rotamer: Outliers : 4.43 % Allowed : 26.08 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.17 (0.20), residues: 1786 helix: -0.69 (0.53), residues: 101 sheet: 0.49 (0.26), residues: 385 loop : -1.27 (0.17), residues: 1300 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 0.013 0.002 PHE E 290 TYR 0.012 0.001 TYR D 223 ARG 0.003 0.000 ARG A 40 ********************** 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 288 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 218 time to evaluate : 1.606 Fit side-chains REVERT: A 11 LYS cc_start: 0.6339 (mmtt) cc_final: 0.5667 (tttm) REVERT: A 41 MET cc_start: 0.7502 (ptm) cc_final: 0.6759 (ptt) REVERT: A 64 ASN cc_start: 0.8582 (p0) cc_final: 0.8319 (p0) REVERT: A 183 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7959 (mtmt) REVERT: A 199 LYS cc_start: 0.8277 (mtpt) cc_final: 0.8062 (mmtt) REVERT: A 238 GLN cc_start: 0.8110 (mt0) cc_final: 0.7835 (mt0) REVERT: A 267 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8742 (p) REVERT: A 270 MET cc_start: 0.8623 (mmm) cc_final: 0.8049 (mmm) REVERT: A 283 TRP cc_start: 0.7762 (OUTLIER) cc_final: 0.6420 (m-10) REVERT: A 316 MET cc_start: 0.2883 (mmm) cc_final: 0.2583 (mmm) REVERT: B 127 LYS cc_start: 0.8011 (tttt) cc_final: 0.7721 (ttmt) REVERT: B 300 LYS cc_start: 0.6759 (mtmt) cc_final: 0.5776 (mmmt) REVERT: C 185 MET cc_start: 0.8782 (mtm) cc_final: 0.8249 (mtm) REVERT: C 258 LYS cc_start: 0.7516 (ptpt) cc_final: 0.6713 (mmtp) REVERT: C 295 ARG cc_start: 0.8668 (ptt180) cc_final: 0.8371 (ptt180) REVERT: D 11 LYS cc_start: 0.8747 (ttpt) cc_final: 0.8494 (tttm) REVERT: D 48 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7209 (mm-30) REVERT: D 176 THR cc_start: 0.8625 (m) cc_final: 0.8099 (p) REVERT: D 238 GLN cc_start: 0.7916 (mt0) cc_final: 0.7661 (mp10) REVERT: E 154 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: E 161 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8051 (tp) REVERT: E 250 GLU cc_start: 0.7311 (tt0) cc_final: 0.6960 (tt0) REVERT: E 305 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8052 (ptm) REVERT: E 326 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6978 (pp20) outliers start: 70 outliers final: 55 residues processed: 267 average time/residue: 1.1107 time to fit residues: 327.5549 Evaluate side-chains 283 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 221 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 VAL 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 350 MET 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 280 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 341 THR 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 40 ARG Chi-restraints excluded: chain C residue 55 GLN 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 D residue 51 THR 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 311 SER Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 46 THR 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 305 MET Chi-restraints excluded: chain E residue 326 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 238 GLN C 102 GLN ** C 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN ** D 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.144842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114887 restraints weight = 14824.737| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.72 r_work: 0.2917 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14351 Z= 0.180 Angle : 0.558 6.560 19569 Z= 0.288 Chirality : 0.043 0.175 2186 Planarity : 0.005 0.060 2552 Dihedral : 6.180 56.856 1944 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.05 % Favored : 92.89 % Rotamer: Outliers : 4.11 % Allowed : 26.58 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.15 (0.20), residues: 1786 helix: -0.94 (0.50), residues: 111 sheet: 0.46 (0.26), residues: 386 loop : -1.22 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.003 0.001 HIS D 282 PHE 0.011 0.001 PHE E 290 TYR 0.010 0.001 TYR D 223 ARG 0.004 0.000 ARG A 40 =============================================================================== Job complete usr+sys time: 6107.84 seconds wall clock time: 106 minutes 39.28 seconds (6399.28 seconds total)