Starting phenix.real_space_refine on Thu May 15 23:21:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yox_33989/05_2025/7yox_33989.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yox_33989/05_2025/7yox_33989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yox_33989/05_2025/7yox_33989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yox_33989/05_2025/7yox_33989.map" model { file = "/net/cci-nas-00/data/ceres_data/7yox_33989/05_2025/7yox_33989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yox_33989/05_2025/7yox_33989.cif" } resolution = 3.95 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 102 5.16 5 C 8745 2.51 5 N 2355 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "C" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "E" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "F" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Time building chain proxies: 8.76, per 1000 atoms: 0.63 Number of scatterers: 13878 At special positions: 0 Unit cell: (77.738, 138.109, 143.071, 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 102 16.00 O 2676 8.00 N 2355 7.00 C 8745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 172 " distance=2.54 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 172 " distance=2.03 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS F 245 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3342 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 17 sheets defined 33.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.901A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.639A pdb=" N THR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.537A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'B' and resid 2 through 21 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 61 through 84 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.761A pdb=" N GLU C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 179 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'D' and resid 2 through 31 removed outlier: 3.763A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 51 through 61 removed outlier: 3.548A pdb=" N GLY D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 84 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.544A pdb=" N GLU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR E 20 " --> pdb=" O TYR E 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN E 23 " --> pdb=" O GLU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 61 through 83 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.811A pdb=" N THR E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 90 through 108 removed outlier: 4.092A pdb=" N GLU F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.704A pdb=" N THR F 135 " --> pdb=" O GLY F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 148 Processing helix chain 'F' and resid 148 through 179 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 365 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 124 removed outlier: 5.686A pdb=" N ILE A 121 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 199 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 123 " --> pdb=" O TYR A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 228 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 218 through 228 current: chain 'A' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 248 through 252 current: chain 'A' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 310 through 316 current: chain 'A' and resid 352 through 364 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 43 removed outlier: 6.784A pdb=" N TYR B 38 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG B 99 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 40 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER B 101 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 42 " --> pdb=" O SER B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 140 removed outlier: 3.546A pdb=" N GLN B 200 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 12.901A pdb=" N SER B 219 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE B 261 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 221 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 241 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 268 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B 239 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL B 130 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 205 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 132 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 143 Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA7, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.017A pdb=" N ILE C 121 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C 199 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 123 " --> pdb=" O TYR C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 205 removed outlier: 3.873A pdb=" N ARG C 222 " --> pdb=" O THR C 205 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 218 through 225 current: chain 'C' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 248 through 252 current: chain 'C' and resid 310 through 315 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 310 through 315 current: chain 'C' and resid 356 through 363 Processing sheet with id=AA9, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 43 removed outlier: 5.483A pdb=" N TYR D 38 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG D 99 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 40 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER D 101 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 42 " --> pdb=" O SER D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 133 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 123 through 133 current: chain 'D' and resid 196 through 205 removed outlier: 3.605A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 219 through 225 current: chain 'D' and resid 259 through 264 Processing sheet with id=AB3, first strand: chain 'D' and resid 142 through 147 removed outlier: 3.605A pdb=" N PHE D 154 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS D 147 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 152 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 43 Processing sheet with id=AB5, first strand: chain 'E' and resid 137 through 139 removed outlier: 8.542A pdb=" N SER E 219 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LEU E 263 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA E 265 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE E 223 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR E 267 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLU E 225 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N GLN E 269 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE E 261 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 247 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E 263 " --> pdb=" O MET E 245 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET E 245 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA E 265 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 243 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL E 130 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN E 205 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 132 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 142 through 146 removed outlier: 4.224A pdb=" N ARG E 143 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 156 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 120 through 124 Processing sheet with id=AB8, first strand: chain 'F' and resid 218 through 221 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 218 through 221 current: chain 'F' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 248 through 252 current: chain 'F' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 310 through 316 current: chain 'F' and resid 355 through 358 No H-bonds generated for sheet with id=AB8 434 hydrogen bonds defined for protein. 1254 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: 3.62 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3992 1.33 - 1.45: 1993 1.45 - 1.57: 8001 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 14133 Sorted by residual: bond pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.28e-02 6.10e+03 6.61e+00 bond pdb=" CA ARG E 247 " pdb=" C ARG E 247 " ideal model delta sigma weight residual 1.521 1.492 0.029 1.19e-02 7.06e+03 6.10e+00 bond pdb=" C ASN D 266 " pdb=" O ASN D 266 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.79e+00 bond pdb=" C LEU F 145 " pdb=" O LEU F 145 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.33e+00 bond pdb=" C PHE E 13 " pdb=" O PHE E 13 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.13e+00 ... (remaining 14128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 17982 2.67 - 5.34: 1013 5.34 - 8.00: 97 8.00 - 10.67: 19 10.67 - 13.34: 2 Bond angle restraints: 19113 Sorted by residual: angle pdb=" N GLN D 162 " pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 112.26 98.92 13.34 1.32e+00 5.74e-01 1.02e+02 angle pdb=" N CYS D 106 " pdb=" CA CYS D 106 " pdb=" C CYS D 106 " ideal model delta sigma weight residual 108.22 101.45 6.77 9.00e-01 1.23e+00 5.65e+01 angle pdb=" N GLY C 132 " pdb=" CA GLY C 132 " pdb=" C GLY C 132 " ideal model delta sigma weight residual 112.73 120.80 -8.07 1.20e+00 6.94e-01 4.52e+01 angle pdb=" N TYR B 20 " pdb=" CA TYR B 20 " pdb=" C TYR B 20 " ideal model delta sigma weight residual 111.36 118.63 -7.27 1.09e+00 8.42e-01 4.44e+01 angle pdb=" N ILE A 93 " pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 110.62 117.15 -6.53 1.02e+00 9.61e-01 4.10e+01 ... (remaining 19108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6568 17.90 - 35.81: 932 35.81 - 53.71: 846 53.71 - 71.61: 334 71.61 - 89.51: 41 Dihedral angle restraints: 8721 sinusoidal: 3573 harmonic: 5148 Sorted by residual: dihedral pdb=" CB CYS F 242 " pdb=" SG CYS F 242 " pdb=" SG CYS F 245 " pdb=" CB CYS F 245 " ideal model delta sinusoidal sigma weight residual 93.00 166.91 -73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" C VAL B 155 " pdb=" N VAL B 155 " pdb=" CA VAL B 155 " pdb=" CB VAL B 155 " ideal model delta harmonic sigma weight residual -122.00 -137.57 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" C PHE C 72 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " pdb=" CB PHE C 72 " ideal model delta harmonic sigma weight residual -122.60 -137.66 15.06 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 8718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1745 0.112 - 0.224: 364 0.224 - 0.335: 54 0.335 - 0.447: 12 0.447 - 0.559: 3 Chirality restraints: 2178 Sorted by residual: chirality pdb=" CA PHE C 72 " pdb=" N PHE C 72 " pdb=" C PHE C 72 " pdb=" CB PHE C 72 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA VAL B 155 " pdb=" N VAL B 155 " pdb=" C VAL B 155 " pdb=" CB VAL B 155 " both_signs ideal model delta sigma weight residual False 2.44 1.96 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA GLU F 202 " pdb=" N GLU F 202 " pdb=" C GLU F 202 " pdb=" CB GLU F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 2175 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO B 39 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 249 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.17e+00 pdb=" N PRO D 250 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 250 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 250 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 168 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO D 169 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " 0.039 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 21 1.61 - 2.43: 133 2.43 - 3.25: 14380 3.25 - 4.08: 42455 4.08 - 4.90: 68604 Warning: very small nonbonded interaction distances. Nonbonded interactions: 125593 Sorted by model distance: nonbonded pdb=" O ILE E 28 " pdb=" CB SER E 91 " model vdw 0.786 3.440 nonbonded pdb=" C ILE E 28 " pdb=" CB SER E 91 " model vdw 0.870 3.670 nonbonded pdb=" CA SER E 18 " pdb=" CE1 HIS E 21 " model vdw 0.903 3.690 nonbonded pdb=" O ILE E 28 " pdb=" OG SER E 91 " model vdw 0.918 3.040 nonbonded pdb=" O LEU B 78 " pdb=" OE1 GLN B 82 " model vdw 0.982 3.040 ... (remaining 125588 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 31.210 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.008 0.512 14138 Z= 0.537 Angle : 1.314 13.945 19121 Z= 0.896 Chirality : 0.095 0.559 2178 Planarity : 0.007 0.074 2466 Dihedral : 27.063 89.513 5367 Min Nonbonded Distance : 0.786 Molprobity Statistics. All-atom Clashscore : 33.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.04 % Favored : 98.79 % Rotamer: Outliers : 46.70 % Allowed : 16.89 % Favored : 36.41 % Cbeta Deviations : 0.48 % 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: 2.84 (0.19), residues: 1737 helix: 3.80 (0.20), residues: 518 sheet: 1.37 (0.25), residues: 426 loop : 0.97 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP F 288 HIS 0.005 0.001 HIS C 195 PHE 0.031 0.003 PHE C 72 TYR 0.024 0.002 TYR C 86 ARG 0.006 0.001 ARG C 146 Details of bonding type rmsd hydrogen bonds : bond 0.17087 ( 434) hydrogen bonds : angle 6.57178 ( 1254) SS BOND : bond 0.25621 ( 4) SS BOND : angle 6.26556 ( 8) covalent geometry : bond 0.00626 (14133) covalent geometry : angle 1.30805 (19113) Misc. bond : bond 0.16164 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 744 poor density : 463 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8393 (pt) REVERT: A 96 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 97 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9117 (tp-100) REVERT: A 112 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7803 (mtpp) REVERT: A 130 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: A 153 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 198 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.5904 (p) REVERT: A 218 TYR cc_start: 0.7766 (t80) cc_final: 0.7257 (t80) REVERT: A 253 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7408 (mp) REVERT: A 288 TRP cc_start: 0.8075 (t60) cc_final: 0.7191 (t60) REVERT: A 300 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.6035 (p0) REVERT: A 314 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: A 332 THR cc_start: 0.6681 (p) cc_final: 0.6044 (p) REVERT: B 21 HIS cc_start: 0.7866 (m90) cc_final: 0.7195 (m90) REVERT: B 78 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 84 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7760 (tp) REVERT: B 92 MET cc_start: 0.7550 (pmm) cc_final: 0.6837 (tmm) REVERT: B 119 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: B 149 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8844 (tptp) REVERT: B 189 LEU cc_start: 0.4581 (OUTLIER) cc_final: 0.4326 (pp) REVERT: B 222 VAL cc_start: 0.8842 (t) cc_final: 0.8133 (t) REVERT: B 239 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8422 (p) REVERT: C 69 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6266 (mt) REVERT: C 78 TRP cc_start: 0.7268 (p-90) cc_final: 0.7032 (p-90) REVERT: C 112 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6836 (mttm) REVERT: C 122 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7941 (pp) REVERT: C 125 PHE cc_start: 0.8112 (t80) cc_final: 0.7910 (t80) REVERT: C 152 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8845 (p) REVERT: C 163 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8268 (t) REVERT: C 187 THR cc_start: 0.4795 (OUTLIER) cc_final: 0.4265 (p) REVERT: C 258 TYR cc_start: 0.7116 (t80) cc_final: 0.6761 (t80) REVERT: C 317 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7697 (t70) REVERT: C 353 PHE cc_start: 0.8352 (m-80) cc_final: 0.8128 (m-80) REVERT: C 361 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7408 (m) REVERT: C 363 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 124 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7911 (pp) REVERT: D 143 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5532 (tpt-90) REVERT: D 145 TYR cc_start: 0.6036 (m-80) cc_final: 0.5544 (m-10) REVERT: D 163 TYR cc_start: 0.7387 (m-10) cc_final: 0.6955 (m-10) REVERT: D 172 CYS cc_start: 0.3736 (OUTLIER) cc_final: 0.1764 (t) REVERT: D 183 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: D 194 THR cc_start: 0.2664 (OUTLIER) cc_final: 0.2154 (t) REVERT: D 254 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8340 (t0) REVERT: E 26 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8294 (pp) REVERT: E 92 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4853 (pmm) REVERT: E 100 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8306 (pp) REVERT: E 120 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8527 (p) REVERT: E 206 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: E 261 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7881 (mt) REVERT: F 63 GLN cc_start: 0.0850 (OUTLIER) cc_final: -0.2429 (tp-100) REVERT: F 65 MET cc_start: 0.1756 (OUTLIER) cc_final: 0.1378 (pmm) REVERT: F 66 GLN cc_start: 0.0813 (OUTLIER) cc_final: 0.0339 (pt0) REVERT: F 69 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.4469 (mm) REVERT: F 78 TRP cc_start: 0.1562 (t-100) cc_final: 0.0667 (t-100) REVERT: F 85 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7843 (p) REVERT: F 93 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8447 (pt) REVERT: F 102 PHE cc_start: 0.8890 (t80) cc_final: 0.8583 (t80) REVERT: F 167 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7050 (t0) REVERT: F 270 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6888 (ptp90) REVERT: F 282 LEU cc_start: 0.9057 (mp) cc_final: 0.8704 (tp) REVERT: F 289 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: F 290 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8032 (t) outliers start: 744 outliers final: 179 residues processed: 980 average time/residue: 0.2882 time to fit residues: 388.2877 Evaluate side-chains 515 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 289 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 270 ARG Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 352 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 71 optimal weight: 0.0050 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 99 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 317 HIS A 339 ASN A 360 ASN B 11 GLN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN C 106 HIS C 136 ASN C 161 HIS C 200 ASN D 2 ASN D 59 ASN D 82 GLN ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 GLN E 269 GLN E 272 ASN F 176 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.103821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.079321 restraints weight = 54038.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.082343 restraints weight = 31242.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084350 restraints weight = 22479.432| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14138 Z= 0.185 Angle : 0.817 11.447 19121 Z= 0.422 Chirality : 0.050 0.335 2178 Planarity : 0.006 0.102 2466 Dihedral : 16.170 89.333 2369 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 14.44 % Allowed : 29.82 % Favored : 55.74 % 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: 1.45 (0.19), residues: 1737 helix: 1.61 (0.21), residues: 521 sheet: 0.86 (0.25), residues: 413 loop : 0.76 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 248 HIS 0.018 0.002 HIS B 37 PHE 0.040 0.003 PHE D 69 TYR 0.024 0.002 TYR F 201 ARG 0.013 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.06012 ( 434) hydrogen bonds : angle 5.81213 ( 1254) SS BOND : bond 0.00563 ( 4) SS BOND : angle 1.42377 ( 8) covalent geometry : bond 0.00413 (14133) covalent geometry : angle 0.81652 (19113) Misc. bond : bond 0.00268 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 282 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8720 (pt) REVERT: A 112 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7567 (mtpp) REVERT: A 198 VAL cc_start: 0.6402 (OUTLIER) cc_final: 0.5537 (p) REVERT: A 218 TYR cc_start: 0.7625 (t80) cc_final: 0.7286 (t80) REVERT: A 332 THR cc_start: 0.6467 (p) cc_final: 0.5828 (p) REVERT: B 21 HIS cc_start: 0.7990 (m90) cc_final: 0.7105 (m90) REVERT: B 31 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6805 (mm-30) REVERT: B 38 TYR cc_start: 0.7319 (m-80) cc_final: 0.6984 (m-80) REVERT: B 48 PHE cc_start: 0.8497 (m-80) cc_final: 0.8087 (m-80) REVERT: B 60 MET cc_start: 0.8779 (ptp) cc_final: 0.8576 (ptp) REVERT: B 69 PHE cc_start: 0.8868 (m-10) cc_final: 0.8471 (m-80) REVERT: B 84 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7951 (tp) REVERT: B 92 MET cc_start: 0.7389 (pmm) cc_final: 0.6804 (tmm) REVERT: B 99 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7362 (mpt180) REVERT: B 149 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8533 (tptp) REVERT: B 209 GLN cc_start: 0.4698 (OUTLIER) cc_final: 0.4485 (pm20) REVERT: C 65 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6450 (ppp) REVERT: C 71 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7642 (tpp-160) REVERT: C 164 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9222 (tm) REVERT: C 302 ARG cc_start: 0.3046 (OUTLIER) cc_final: 0.2262 (pmt-80) REVERT: C 314 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7216 (mp0) REVERT: D 145 TYR cc_start: 0.6604 (m-80) cc_final: 0.6353 (m-10) REVERT: D 254 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.9004 (t0) REVERT: D 258 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8069 (pt0) REVERT: E 60 MET cc_start: 0.8301 (tpp) cc_final: 0.8070 (tpp) REVERT: E 164 TYR cc_start: 0.6311 (t80) cc_final: 0.5673 (t80) REVERT: E 187 SER cc_start: 0.3974 (OUTLIER) cc_final: 0.3633 (t) REVERT: E 202 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8409 (mt) REVERT: E 225 GLU cc_start: 0.8209 (tp30) cc_final: 0.7716 (mp0) REVERT: E 241 TYR cc_start: 0.8206 (m-10) cc_final: 0.7954 (m-10) REVERT: F 85 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8017 (p) REVERT: F 95 LYS cc_start: 0.9362 (mtmp) cc_final: 0.9071 (mttm) REVERT: F 106 HIS cc_start: 0.8233 (m90) cc_final: 0.7912 (m90) REVERT: F 112 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8489 (mtmt) REVERT: F 171 HIS cc_start: 0.7731 (m170) cc_final: 0.7381 (m90) REVERT: F 238 MET cc_start: 0.8214 (tpp) cc_final: 0.7932 (tpp) REVERT: F 282 LEU cc_start: 0.9106 (mp) cc_final: 0.8638 (tp) REVERT: F 289 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: F 291 ILE cc_start: 0.8877 (pt) cc_final: 0.8532 (pt) REVERT: F 314 GLU cc_start: 0.8319 (mp0) cc_final: 0.7729 (mp0) outliers start: 230 outliers final: 123 residues processed: 463 average time/residue: 0.2429 time to fit residues: 163.4518 Evaluate side-chains 375 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 233 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 ASN ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN D 266 ASN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN E 253 GLN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN F 289 GLN F 346 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.100098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.075729 restraints weight = 56606.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.078401 restraints weight = 33555.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.080158 restraints weight = 24794.070| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14138 Z= 0.184 Angle : 0.724 13.182 19121 Z= 0.376 Chirality : 0.047 0.179 2178 Planarity : 0.005 0.061 2466 Dihedral : 12.411 83.930 2099 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 11.49 % Allowed : 30.01 % Favored : 58.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 1737 helix: 1.26 (0.22), residues: 514 sheet: 0.63 (0.25), residues: 418 loop : 0.66 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 288 HIS 0.014 0.001 HIS B 37 PHE 0.042 0.003 PHE D 69 TYR 0.026 0.002 TYR E 267 ARG 0.008 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.05057 ( 434) hydrogen bonds : angle 5.54655 ( 1254) SS BOND : bond 0.00422 ( 4) SS BOND : angle 0.96019 ( 8) covalent geometry : bond 0.00403 (14133) covalent geometry : angle 0.72377 (19113) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 247 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7642 (ttpt) REVERT: A 118 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6328 (pttm) REVERT: A 195 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7222 (p90) REVERT: A 198 VAL cc_start: 0.6576 (OUTLIER) cc_final: 0.5874 (p) REVERT: A 218 TYR cc_start: 0.7646 (t80) cc_final: 0.7295 (t80) REVERT: A 286 MET cc_start: 0.8523 (tpp) cc_final: 0.8300 (tpp) REVERT: A 297 MET cc_start: 0.5857 (mmm) cc_final: 0.5467 (mmm) REVERT: A 319 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8996 (mm) REVERT: A 332 THR cc_start: 0.6322 (p) cc_final: 0.5885 (p) REVERT: B 48 PHE cc_start: 0.8415 (m-80) cc_final: 0.7604 (m-80) REVERT: B 52 MET cc_start: 0.7797 (pmm) cc_final: 0.6475 (mmm) REVERT: B 60 MET cc_start: 0.8975 (ptp) cc_final: 0.8763 (ptp) REVERT: B 69 PHE cc_start: 0.8946 (m-10) cc_final: 0.8452 (m-80) REVERT: B 84 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 92 MET cc_start: 0.7425 (pmm) cc_final: 0.6829 (tmm) REVERT: B 161 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8078 (mm-30) REVERT: B 209 GLN cc_start: 0.5496 (OUTLIER) cc_final: 0.5283 (pm20) REVERT: C 65 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6862 (ppp) REVERT: C 71 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7825 (tpp-160) REVERT: C 125 PHE cc_start: 0.8023 (t80) cc_final: 0.7621 (t80) REVERT: C 164 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9203 (tm) REVERT: C 302 ARG cc_start: 0.3490 (OUTLIER) cc_final: 0.2475 (pmt-80) REVERT: C 314 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7349 (mp0) REVERT: D 45 MET cc_start: 0.8843 (ppp) cc_final: 0.8351 (ppp) REVERT: D 93 LYS cc_start: 0.4271 (OUTLIER) cc_final: 0.4018 (mmtm) REVERT: D 97 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7893 (m170) REVERT: D 145 TYR cc_start: 0.7233 (m-80) cc_final: 0.6837 (m-10) REVERT: D 205 GLN cc_start: 0.8287 (pp30) cc_final: 0.7939 (pp30) REVERT: D 237 ASP cc_start: 0.8122 (m-30) cc_final: 0.7869 (m-30) REVERT: D 254 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8906 (t0) REVERT: E 157 LYS cc_start: 0.7645 (mmtm) cc_final: 0.7054 (ttpt) REVERT: E 161 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: F 85 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8046 (p) REVERT: F 106 HIS cc_start: 0.8253 (m90) cc_final: 0.7922 (m90) REVERT: F 161 HIS cc_start: 0.8751 (t70) cc_final: 0.8486 (t70) REVERT: F 238 MET cc_start: 0.7964 (tpp) cc_final: 0.7696 (tpp) outliers start: 183 outliers final: 115 residues processed: 395 average time/residue: 0.2348 time to fit residues: 136.6748 Evaluate side-chains 348 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 217 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 PHE Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0670 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 overall best weight: 3.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 171 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS D 266 ASN D 269 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.098766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.074154 restraints weight = 56390.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.076663 restraints weight = 34400.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.078264 restraints weight = 25943.420| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14138 Z= 0.182 Angle : 0.697 12.851 19121 Z= 0.360 Chirality : 0.046 0.190 2178 Planarity : 0.005 0.073 2466 Dihedral : 10.666 85.424 2033 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 10.42 % Allowed : 30.95 % Favored : 58.63 % 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: 0.84 (0.20), residues: 1737 helix: 1.01 (0.22), residues: 513 sheet: 0.36 (0.25), residues: 417 loop : 0.56 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 248 HIS 0.007 0.001 HIS E 21 PHE 0.051 0.003 PHE D 69 TYR 0.031 0.002 TYR F 356 ARG 0.006 0.001 ARG A 278 Details of bonding type rmsd hydrogen bonds : bond 0.04715 ( 434) hydrogen bonds : angle 5.44966 ( 1254) SS BOND : bond 0.00716 ( 4) SS BOND : angle 2.98144 ( 8) covalent geometry : bond 0.00400 (14133) covalent geometry : angle 0.69413 (19113) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 227 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7592 (ttpt) REVERT: A 158 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.5945 (tp) REVERT: A 195 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7398 (p90) REVERT: A 198 VAL cc_start: 0.6665 (OUTLIER) cc_final: 0.6194 (p) REVERT: A 297 MET cc_start: 0.5849 (mmm) cc_final: 0.5507 (mmm) REVERT: A 319 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 332 THR cc_start: 0.6414 (p) cc_final: 0.6185 (p) REVERT: B 21 HIS cc_start: 0.8179 (m-70) cc_final: 0.7384 (m90) REVERT: B 38 TYR cc_start: 0.7747 (m-80) cc_final: 0.7466 (m-80) REVERT: B 48 PHE cc_start: 0.8348 (m-80) cc_final: 0.7720 (m-10) REVERT: B 52 MET cc_start: 0.7863 (pmm) cc_final: 0.6538 (mmm) REVERT: B 69 PHE cc_start: 0.8998 (m-10) cc_final: 0.8716 (m-80) REVERT: B 92 MET cc_start: 0.7246 (pmm) cc_final: 0.6479 (ppp) REVERT: B 149 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8485 (tptp) REVERT: B 161 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 164 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7766 (t80) REVERT: B 209 GLN cc_start: 0.5530 (OUTLIER) cc_final: 0.5308 (pm20) REVERT: C 65 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6929 (ppp) REVERT: C 125 PHE cc_start: 0.8156 (t80) cc_final: 0.7816 (t80) REVERT: C 155 CYS cc_start: 0.8817 (t) cc_final: 0.8600 (t) REVERT: C 164 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9254 (tm) REVERT: C 238 MET cc_start: 0.8110 (tpp) cc_final: 0.7674 (tpp) REVERT: C 247 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: C 302 ARG cc_start: 0.3917 (OUTLIER) cc_final: 0.2898 (pmt-80) REVERT: D 45 MET cc_start: 0.8897 (ppp) cc_final: 0.8500 (ppp) REVERT: D 93 LYS cc_start: 0.4455 (OUTLIER) cc_final: 0.4164 (mmtm) REVERT: D 145 TYR cc_start: 0.7477 (m-80) cc_final: 0.7003 (m-10) REVERT: D 237 ASP cc_start: 0.8170 (m-30) cc_final: 0.7873 (m-30) REVERT: E 157 LYS cc_start: 0.7643 (mmtm) cc_final: 0.6976 (ttpp) REVERT: E 161 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7959 (mm-30) REVERT: E 164 TYR cc_start: 0.6970 (t80) cc_final: 0.5823 (t80) REVERT: F 106 HIS cc_start: 0.8315 (m90) cc_final: 0.8088 (m90) REVERT: F 161 HIS cc_start: 0.8866 (t70) cc_final: 0.8520 (t70) REVERT: F 238 MET cc_start: 0.8129 (tpp) cc_final: 0.7908 (tpp) outliers start: 166 outliers final: 119 residues processed: 358 average time/residue: 0.2269 time to fit residues: 122.5243 Evaluate side-chains 337 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 204 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 267 TYR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 PHE Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 77 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.096132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.072681 restraints weight = 59021.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.073823 restraints weight = 39739.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.074647 restraints weight = 31899.132| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14138 Z= 0.211 Angle : 0.698 13.052 19121 Z= 0.367 Chirality : 0.046 0.198 2178 Planarity : 0.005 0.079 2466 Dihedral : 10.065 86.600 2011 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 27.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 10.17 % Allowed : 31.89 % Favored : 57.94 % 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: 0.40 (0.20), residues: 1737 helix: 0.66 (0.22), residues: 519 sheet: -0.08 (0.26), residues: 381 loop : 0.38 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP D 248 HIS 0.008 0.001 HIS E 21 PHE 0.048 0.003 PHE E 13 TYR 0.019 0.002 TYR B 164 ARG 0.007 0.001 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 434) hydrogen bonds : angle 5.57641 ( 1254) SS BOND : bond 0.00569 ( 4) SS BOND : angle 2.30407 ( 8) covalent geometry : bond 0.00458 (14133) covalent geometry : angle 0.69701 (19113) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 211 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8355 (mppt) REVERT: A 195 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7345 (p90) REVERT: A 297 MET cc_start: 0.6000 (mmm) cc_final: 0.5706 (mmm) REVERT: B 32 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6424 (ptp90) REVERT: B 48 PHE cc_start: 0.8350 (m-80) cc_final: 0.7605 (m-80) REVERT: B 52 MET cc_start: 0.7947 (pmm) cc_final: 0.6697 (mmt) REVERT: B 69 PHE cc_start: 0.9154 (m-10) cc_final: 0.8889 (m-80) REVERT: B 92 MET cc_start: 0.7076 (pmm) cc_final: 0.6416 (ppp) REVERT: B 149 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8472 (tptp) REVERT: B 161 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7749 (mm-30) REVERT: B 164 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7912 (t80) REVERT: B 209 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5584 (pm20) REVERT: C 65 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6952 (ppp) REVERT: C 125 PHE cc_start: 0.8176 (t80) cc_final: 0.7915 (t80) REVERT: C 164 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9237 (tm) REVERT: D 45 MET cc_start: 0.8962 (ppp) cc_final: 0.8491 (ppp) REVERT: D 93 LYS cc_start: 0.4956 (OUTLIER) cc_final: 0.4732 (mmtt) REVERT: D 145 TYR cc_start: 0.7745 (m-80) cc_final: 0.7195 (m-10) REVERT: E 157 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7338 (ttmt) REVERT: E 164 TYR cc_start: 0.7332 (t80) cc_final: 0.6314 (t80) REVERT: F 106 HIS cc_start: 0.8473 (m90) cc_final: 0.8179 (m90) REVERT: F 125 PHE cc_start: 0.7227 (t80) cc_final: 0.6903 (t80) REVERT: F 358 GLU cc_start: 0.8664 (pp20) cc_final: 0.8416 (pp20) outliers start: 162 outliers final: 123 residues processed: 346 average time/residue: 0.2141 time to fit residues: 112.1779 Evaluate side-chains 330 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 198 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 301 GLN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 PHE Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 138 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 HIS C 317 HIS D 274 GLN ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.095473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071322 restraints weight = 58360.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073575 restraints weight = 37174.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.075005 restraints weight = 28617.045| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14138 Z= 0.218 Angle : 0.690 13.254 19121 Z= 0.362 Chirality : 0.046 0.177 2178 Planarity : 0.005 0.073 2466 Dihedral : 9.330 58.859 1992 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 9.98 % Allowed : 32.71 % Favored : 57.31 % 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: 0.14 (0.20), residues: 1737 helix: 0.55 (0.22), residues: 518 sheet: -0.31 (0.26), residues: 379 loop : 0.18 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 248 HIS 0.008 0.001 HIS E 21 PHE 0.044 0.003 PHE D 69 TYR 0.022 0.002 TYR E 267 ARG 0.009 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 434) hydrogen bonds : angle 5.65407 ( 1254) SS BOND : bond 0.00390 ( 4) SS BOND : angle 1.92702 ( 8) covalent geometry : bond 0.00471 (14133) covalent geometry : angle 0.68947 (19113) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 203 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8384 (mppt) REVERT: A 118 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6460 (ttpp) REVERT: A 160 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8122 (tp) REVERT: A 195 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7769 (p90) REVERT: A 297 MET cc_start: 0.5922 (mmm) cc_final: 0.5541 (mmm) REVERT: B 32 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.6611 (ptp90) REVERT: B 51 ASN cc_start: 0.7838 (t0) cc_final: 0.7459 (t0) REVERT: B 52 MET cc_start: 0.7981 (pmm) cc_final: 0.6879 (mmt) REVERT: B 69 PHE cc_start: 0.9103 (m-10) cc_final: 0.8828 (m-80) REVERT: B 92 MET cc_start: 0.7369 (pmm) cc_final: 0.6759 (ppp) REVERT: B 149 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8438 (tptp) REVERT: B 161 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 164 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8012 (t80) REVERT: C 65 MET cc_start: 0.7417 (mtm) cc_final: 0.6917 (ppp) REVERT: C 108 ASP cc_start: 0.8247 (p0) cc_final: 0.7887 (p0) REVERT: C 164 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9252 (tm) REVERT: C 238 MET cc_start: 0.8223 (tpp) cc_final: 0.7747 (tpp) REVERT: C 302 ARG cc_start: 0.4129 (OUTLIER) cc_final: 0.0709 (pmt-80) REVERT: D 45 MET cc_start: 0.8914 (ppp) cc_final: 0.8394 (ppp) REVERT: D 93 LYS cc_start: 0.4510 (OUTLIER) cc_final: 0.4235 (mmtt) REVERT: D 145 TYR cc_start: 0.7520 (m-80) cc_final: 0.7094 (m-10) REVERT: D 225 GLU cc_start: 0.8483 (mp0) cc_final: 0.8153 (mp0) REVERT: D 254 ASP cc_start: 0.9088 (t0) cc_final: 0.8781 (t0) REVERT: D 274 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7465 (mm-40) REVERT: E 135 LEU cc_start: 0.7796 (pt) cc_final: 0.7508 (pp) REVERT: E 157 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7421 (ttmt) REVERT: F 106 HIS cc_start: 0.8558 (m90) cc_final: 0.8127 (m90) REVERT: F 125 PHE cc_start: 0.7180 (t80) cc_final: 0.5963 (t80) REVERT: F 358 GLU cc_start: 0.8649 (pp20) cc_final: 0.8344 (pp20) outliers start: 159 outliers final: 122 residues processed: 333 average time/residue: 0.2259 time to fit residues: 113.2061 Evaluate side-chains 321 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 188 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 61 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 45 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 164 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.095427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071266 restraints weight = 58390.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073507 restraints weight = 37092.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.074957 restraints weight = 28544.673| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.7339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14138 Z= 0.201 Angle : 0.707 13.666 19121 Z= 0.366 Chirality : 0.046 0.259 2178 Planarity : 0.005 0.060 2466 Dihedral : 8.971 59.973 1985 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 8.98 % Allowed : 34.21 % Favored : 56.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1737 helix: 0.41 (0.22), residues: 526 sheet: -0.30 (0.26), residues: 398 loop : 0.19 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP D 248 HIS 0.012 0.001 HIS C 195 PHE 0.052 0.003 PHE E 13 TYR 0.039 0.002 TYR C 199 ARG 0.010 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04610 ( 434) hydrogen bonds : angle 5.70410 ( 1254) SS BOND : bond 0.00361 ( 4) SS BOND : angle 1.85751 ( 8) covalent geometry : bond 0.00439 (14133) covalent geometry : angle 0.70632 (19113) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 193 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7595 (ttpt) REVERT: A 118 LYS cc_start: 0.6679 (OUTLIER) cc_final: 0.6385 (ttpp) REVERT: A 195 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7762 (p90) REVERT: A 297 MET cc_start: 0.6077 (mmm) cc_final: 0.5768 (mmm) REVERT: B 32 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6743 (ptp90) REVERT: B 38 TYR cc_start: 0.7964 (m-80) cc_final: 0.7601 (m-80) REVERT: B 51 ASN cc_start: 0.7852 (t0) cc_final: 0.7487 (t0) REVERT: B 52 MET cc_start: 0.7970 (pmm) cc_final: 0.7041 (mmt) REVERT: B 60 MET cc_start: 0.8984 (ptt) cc_final: 0.8481 (tmm) REVERT: B 69 PHE cc_start: 0.9124 (m-10) cc_final: 0.8853 (m-80) REVERT: B 92 MET cc_start: 0.7310 (pmm) cc_final: 0.6685 (ppp) REVERT: B 161 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 164 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7988 (t80) REVERT: C 65 MET cc_start: 0.7375 (mtm) cc_final: 0.6915 (ppp) REVERT: C 108 ASP cc_start: 0.8246 (p0) cc_final: 0.7926 (p0) REVERT: C 164 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9234 (tm) REVERT: C 238 MET cc_start: 0.8224 (tpp) cc_final: 0.7805 (tpp) REVERT: C 302 ARG cc_start: 0.4144 (OUTLIER) cc_final: 0.0730 (pmt-80) REVERT: D 45 MET cc_start: 0.8858 (ppp) cc_final: 0.8363 (ppp) REVERT: D 93 LYS cc_start: 0.4431 (OUTLIER) cc_final: 0.3994 (mmtt) REVERT: D 145 TYR cc_start: 0.7450 (m-80) cc_final: 0.7044 (m-10) REVERT: D 254 ASP cc_start: 0.9019 (t0) cc_final: 0.8723 (t0) REVERT: D 274 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7280 (mm-40) REVERT: E 60 MET cc_start: 0.8628 (tpp) cc_final: 0.8405 (tpp) REVERT: E 135 LEU cc_start: 0.7796 (pt) cc_final: 0.7458 (pp) REVERT: E 157 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7506 (ttmt) REVERT: E 161 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8182 (mm-30) REVERT: E 198 ASP cc_start: 0.8552 (p0) cc_final: 0.8157 (p0) REVERT: F 106 HIS cc_start: 0.8527 (m90) cc_final: 0.8059 (m90) REVERT: F 358 GLU cc_start: 0.8646 (pp20) cc_final: 0.8291 (pp20) outliers start: 143 outliers final: 111 residues processed: 315 average time/residue: 0.2262 time to fit residues: 108.0587 Evaluate side-chains 307 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 186 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 30 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.096339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.072191 restraints weight = 57568.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074458 restraints weight = 36372.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.075895 restraints weight = 27924.096| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.7563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14138 Z= 0.167 Angle : 0.697 13.253 19121 Z= 0.358 Chirality : 0.046 0.248 2178 Planarity : 0.005 0.060 2466 Dihedral : 8.436 59.558 1969 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 8.10 % Allowed : 34.78 % Favored : 57.12 % 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: 0.08 (0.20), residues: 1737 helix: 0.51 (0.22), residues: 515 sheet: -0.39 (0.26), residues: 404 loop : 0.19 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 248 HIS 0.011 0.001 HIS C 195 PHE 0.055 0.003 PHE E 13 TYR 0.027 0.002 TYR E 267 ARG 0.017 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 434) hydrogen bonds : angle 5.67049 ( 1254) SS BOND : bond 0.00356 ( 4) SS BOND : angle 1.88348 ( 8) covalent geometry : bond 0.00369 (14133) covalent geometry : angle 0.69639 (19113) Misc. bond : bond 0.00113 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 194 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7623 (ttpt) REVERT: A 195 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7730 (p90) REVERT: A 297 MET cc_start: 0.6035 (mmm) cc_final: 0.5571 (mmm) REVERT: B 21 HIS cc_start: 0.8416 (m90) cc_final: 0.7897 (m90) REVERT: B 32 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6842 (ptp90) REVERT: B 38 TYR cc_start: 0.7846 (m-80) cc_final: 0.7446 (m-80) REVERT: B 51 ASN cc_start: 0.7818 (t0) cc_final: 0.7475 (t0) REVERT: B 52 MET cc_start: 0.7950 (pmm) cc_final: 0.7036 (mmt) REVERT: B 57 TYR cc_start: 0.9318 (m-80) cc_final: 0.8776 (m-80) REVERT: B 69 PHE cc_start: 0.9104 (m-10) cc_final: 0.8836 (m-80) REVERT: B 92 MET cc_start: 0.7374 (pmm) cc_final: 0.6742 (ppp) REVERT: B 161 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 164 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7927 (t80) REVERT: C 65 MET cc_start: 0.7382 (mtm) cc_final: 0.6946 (ppp) REVERT: C 108 ASP cc_start: 0.8252 (p0) cc_final: 0.7974 (p0) REVERT: C 117 ARG cc_start: 0.9102 (ptm160) cc_final: 0.8865 (ptm160) REVERT: C 164 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9240 (tm) REVERT: C 238 MET cc_start: 0.8094 (tpp) cc_final: 0.7622 (tpp) REVERT: C 302 ARG cc_start: 0.3961 (OUTLIER) cc_final: 0.0585 (pmt-80) REVERT: C 353 PHE cc_start: 0.8371 (m-80) cc_final: 0.7944 (m-10) REVERT: D 45 MET cc_start: 0.8810 (ppp) cc_final: 0.8333 (ppp) REVERT: D 145 TYR cc_start: 0.7425 (m-80) cc_final: 0.7163 (m-10) REVERT: D 254 ASP cc_start: 0.8977 (t0) cc_final: 0.8679 (t0) REVERT: D 274 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7262 (mm-40) REVERT: E 60 MET cc_start: 0.8603 (tpp) cc_final: 0.8276 (tpp) REVERT: E 135 LEU cc_start: 0.7628 (pt) cc_final: 0.7332 (pp) REVERT: E 157 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7371 (ttpt) REVERT: E 161 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: E 164 TYR cc_start: 0.7214 (t80) cc_final: 0.6088 (t80) REVERT: E 198 ASP cc_start: 0.8501 (p0) cc_final: 0.8158 (p0) REVERT: E 199 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8369 (t80) REVERT: F 106 HIS cc_start: 0.8552 (m90) cc_final: 0.8057 (m90) REVERT: F 297 MET cc_start: 0.7106 (mpp) cc_final: 0.6697 (mpp) REVERT: F 358 GLU cc_start: 0.8609 (pp20) cc_final: 0.8232 (pp20) outliers start: 129 outliers final: 102 residues processed: 302 average time/residue: 0.2169 time to fit residues: 98.5777 Evaluate side-chains 295 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 184 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 62 optimal weight: 0.8980 chunk 141 optimal weight: 30.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.098726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.074695 restraints weight = 55453.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.077113 restraints weight = 33719.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.078710 restraints weight = 25218.174| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.7684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14138 Z= 0.128 Angle : 0.717 13.937 19121 Z= 0.359 Chirality : 0.048 0.326 2178 Planarity : 0.004 0.057 2466 Dihedral : 7.881 57.620 1965 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.40 % Allowed : 36.79 % Favored : 56.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1737 helix: 0.51 (0.22), residues: 515 sheet: -0.35 (0.25), residues: 419 loop : 0.26 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 248 HIS 0.010 0.001 HIS C 195 PHE 0.061 0.003 PHE E 13 TYR 0.033 0.002 TYR E 267 ARG 0.012 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 434) hydrogen bonds : angle 5.55148 ( 1254) SS BOND : bond 0.00415 ( 4) SS BOND : angle 1.81410 ( 8) covalent geometry : bond 0.00286 (14133) covalent geometry : angle 0.71655 (19113) Misc. bond : bond 0.00094 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 208 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7640 (ttpt) REVERT: A 195 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7816 (p90) REVERT: A 297 MET cc_start: 0.5974 (mmm) cc_final: 0.5657 (mmm) REVERT: B 21 HIS cc_start: 0.8376 (m90) cc_final: 0.7916 (m90) REVERT: B 32 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.6643 (ptp90) REVERT: B 38 TYR cc_start: 0.7560 (m-80) cc_final: 0.7145 (m-80) REVERT: B 45 MET cc_start: 0.8540 (ppp) cc_final: 0.8093 (pmm) REVERT: B 48 PHE cc_start: 0.8107 (m-80) cc_final: 0.7200 (m-80) REVERT: B 51 ASN cc_start: 0.7762 (t0) cc_final: 0.7466 (t0) REVERT: B 52 MET cc_start: 0.7831 (pmm) cc_final: 0.6948 (mmt) REVERT: B 57 TYR cc_start: 0.9301 (m-80) cc_final: 0.8796 (m-80) REVERT: B 69 PHE cc_start: 0.9001 (m-10) cc_final: 0.8798 (m-80) REVERT: B 92 MET cc_start: 0.7350 (pmm) cc_final: 0.6750 (ppp) REVERT: B 161 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7829 (mm-30) REVERT: B 164 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7801 (t80) REVERT: C 65 MET cc_start: 0.7389 (mtm) cc_final: 0.7012 (ppp) REVERT: C 78 TRP cc_start: 0.7445 (p-90) cc_final: 0.6924 (p-90) REVERT: C 108 ASP cc_start: 0.8312 (p0) cc_final: 0.8027 (p0) REVERT: C 117 ARG cc_start: 0.9060 (ptm160) cc_final: 0.8795 (ptm160) REVERT: C 164 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9207 (tm) REVERT: C 238 MET cc_start: 0.7837 (tpp) cc_final: 0.7461 (tpp) REVERT: C 353 PHE cc_start: 0.8257 (m-80) cc_final: 0.7874 (m-10) REVERT: D 45 MET cc_start: 0.8742 (ppp) cc_final: 0.8309 (ppp) REVERT: D 145 TYR cc_start: 0.7402 (m-80) cc_final: 0.7080 (m-10) REVERT: D 254 ASP cc_start: 0.8944 (t0) cc_final: 0.8624 (t0) REVERT: E 157 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7150 (ttpt) REVERT: E 164 TYR cc_start: 0.6867 (t80) cc_final: 0.5744 (t80) REVERT: E 198 ASP cc_start: 0.8395 (p0) cc_final: 0.8052 (p0) REVERT: F 106 HIS cc_start: 0.8504 (m90) cc_final: 0.7288 (m90) REVERT: F 110 TYR cc_start: 0.8009 (m-80) cc_final: 0.7658 (m-80) REVERT: F 297 MET cc_start: 0.7059 (mpp) cc_final: 0.6514 (mpp) REVERT: F 358 GLU cc_start: 0.8556 (pp20) cc_final: 0.8190 (pp20) outliers start: 102 outliers final: 89 residues processed: 291 average time/residue: 0.2357 time to fit residues: 104.5479 Evaluate side-chains 286 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 192 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 138 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 68 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS F 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.096845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.073363 restraints weight = 59001.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.074057 restraints weight = 39805.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.074805 restraints weight = 31696.893| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14138 Z= 0.155 Angle : 0.717 14.019 19121 Z= 0.364 Chirality : 0.047 0.268 2178 Planarity : 0.005 0.057 2466 Dihedral : 7.752 58.983 1958 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.21 % Allowed : 37.29 % Favored : 56.50 % 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: 0.12 (0.20), residues: 1737 helix: 0.56 (0.22), residues: 515 sheet: -0.38 (0.26), residues: 403 loop : 0.20 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 248 HIS 0.009 0.001 HIS C 195 PHE 0.053 0.003 PHE E 13 TYR 0.032 0.002 TYR E 267 ARG 0.011 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 434) hydrogen bonds : angle 5.58345 ( 1254) SS BOND : bond 0.00351 ( 4) SS BOND : angle 1.71956 ( 8) covalent geometry : bond 0.00347 (14133) covalent geometry : angle 0.71638 (19113) Misc. bond : bond 0.00179 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 190 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8680 (mmtt) cc_final: 0.7672 (ttpt) REVERT: A 195 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7728 (p90) REVERT: A 297 MET cc_start: 0.6503 (mmm) cc_final: 0.6066 (mmm) REVERT: B 21 HIS cc_start: 0.8675 (m90) cc_final: 0.8113 (m90) REVERT: B 32 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.6810 (ptp90) REVERT: B 38 TYR cc_start: 0.7855 (m-80) cc_final: 0.7346 (m-80) REVERT: B 45 MET cc_start: 0.8667 (ppp) cc_final: 0.8166 (pmm) REVERT: B 51 ASN cc_start: 0.8042 (t0) cc_final: 0.7552 (t0) REVERT: B 52 MET cc_start: 0.7974 (pmm) cc_final: 0.7015 (mmt) REVERT: B 57 TYR cc_start: 0.9445 (m-80) cc_final: 0.8852 (m-80) REVERT: B 69 PHE cc_start: 0.9196 (m-10) cc_final: 0.8967 (m-80) REVERT: B 92 MET cc_start: 0.7047 (pmm) cc_final: 0.6535 (ppp) REVERT: B 161 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7865 (mm-30) REVERT: B 164 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7891 (t80) REVERT: C 65 MET cc_start: 0.7374 (mtm) cc_final: 0.7059 (ppp) REVERT: C 108 ASP cc_start: 0.8332 (p0) cc_final: 0.8077 (p0) REVERT: C 164 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9225 (tm) REVERT: C 238 MET cc_start: 0.8300 (tpp) cc_final: 0.7740 (tpp) REVERT: C 353 PHE cc_start: 0.8339 (m-80) cc_final: 0.7928 (m-10) REVERT: D 45 MET cc_start: 0.8849 (ppp) cc_final: 0.8379 (ppp) REVERT: D 145 TYR cc_start: 0.7695 (m-80) cc_final: 0.7232 (m-10) REVERT: D 254 ASP cc_start: 0.9052 (t0) cc_final: 0.8739 (t0) REVERT: E 135 LEU cc_start: 0.7567 (pt) cc_final: 0.7300 (pp) REVERT: E 157 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7377 (ttmt) REVERT: E 161 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: E 164 TYR cc_start: 0.7243 (t80) cc_final: 0.6014 (t80) REVERT: E 198 ASP cc_start: 0.8513 (p0) cc_final: 0.8151 (p0) REVERT: E 260 GLU cc_start: 0.8175 (tp30) cc_final: 0.7765 (tp30) REVERT: F 110 TYR cc_start: 0.8148 (m-80) cc_final: 0.7661 (m-80) REVERT: F 297 MET cc_start: 0.7463 (mpp) cc_final: 0.6898 (mpp) REVERT: F 358 GLU cc_start: 0.8613 (pp20) cc_final: 0.8221 (pp20) outliers start: 99 outliers final: 88 residues processed: 275 average time/residue: 0.2173 time to fit residues: 92.1306 Evaluate side-chains 280 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 187 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 106 HIS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 248 TRP Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 20 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 HIS F 294 GLN F 339 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.098525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.073612 restraints weight = 57725.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.076037 restraints weight = 35626.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.077608 restraints weight = 26954.328| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14138 Z= 0.130 Angle : 0.731 13.861 19121 Z= 0.364 Chirality : 0.047 0.286 2178 Planarity : 0.004 0.055 2466 Dihedral : 7.507 57.377 1954 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.78 % Allowed : 37.85 % Favored : 56.37 % 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: 0.19 (0.20), residues: 1737 helix: 0.60 (0.22), residues: 509 sheet: -0.30 (0.25), residues: 419 loop : 0.25 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 248 HIS 0.012 0.001 HIS C 106 PHE 0.055 0.003 PHE E 13 TYR 0.031 0.002 TYR E 267 ARG 0.011 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 434) hydrogen bonds : angle 5.53354 ( 1254) SS BOND : bond 0.00379 ( 4) SS BOND : angle 1.70364 ( 8) covalent geometry : bond 0.00292 (14133) covalent geometry : angle 0.73040 (19113) Misc. bond : bond 0.00097 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5533.83 seconds wall clock time: 97 minutes 48.03 seconds (5868.03 seconds total)