Starting phenix.real_space_refine on Thu Aug 6 22:18:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn2_52305/08_2026/9hn2_52305.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn2_52305/08_2026/9hn2_52305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hn2_52305/08_2026/9hn2_52305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn2_52305/08_2026/9hn2_52305.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn2_52305/08_2026/9hn2_52305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn2_52305/08_2026/9hn2_52305.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.085 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: 5 Type Number sf(0) Gaussians S 21 5.16 5 C 5546 2.51 5 N 1508 2.21 5 O 1804 1.98 5 H 8154 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17033 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 4936 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 326} Chain breaks: 3 Chain: "B" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 4946 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 327} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 5005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5005 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 332} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2146 Classifications: {'peptide': 143} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 3.26, per 1000 atoms: 0.19 Number of scatterers: 17033 At special positions: 0 Unit cell: (123.975, 94.05, 92.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 O 1804 8.00 N 1508 7.00 C 5546 6.00 H 8154 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 561.8 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 13.4% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.965A pdb=" N GLU A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 339 through 345 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.930A pdb=" N GLU B 124 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.856A pdb=" N GLU C 124 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.735A pdb=" N THR C 146 " --> pdb=" O ASN C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.557A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 124 Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 132 through 146 removed outlier: 3.783A pdb=" N GLN D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 236 removed outlier: 3.850A pdb=" N ALA D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Proline residue: D 219 - end of helix removed outlier: 3.827A pdb=" N ASN D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 293 removed outlier: 3.995A pdb=" N ALA D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 284 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 32 through 34 current: chain 'A' and resid 53 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 53 through 54 current: chain 'A' and resid 74 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 94 through 95 current: chain 'A' and resid 110 through 115 removed outlier: 4.036A pdb=" N GLY A 190 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 314 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 328 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 326 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 4.287A pdb=" N TYR B 26 " --> pdb=" O LEU B 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 31 through 33 current: chain 'B' and resid 53 through 55 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 53 through 55 current: chain 'B' and resid 73 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 94 through 95 current: chain 'B' and resid 110 through 116 removed outlier: 6.557A pdb=" N ASN B 116 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASN B 150 " --> pdb=" O ASN B 116 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER B 284 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL B 314 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 286 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 312 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 288 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS B 310 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 290 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 24 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 24 through 27 current: chain 'C' and resid 75 through 84 removed outlier: 7.314A pdb=" N TYR C 76 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA C 101 " --> pdb=" O TYR C 76 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLN C 78 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA C 99 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU C 80 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 12.561A pdb=" N ARG C 97 " --> pdb=" O TYR C 117 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR C 117 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN C 116 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASN C 150 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE C 285 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL C 314 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR C 287 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 312 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLN C 289 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS C 310 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS C 291 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU C 308 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS C 293 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA C 306 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY C 304 " --> pdb=" O LEU C 295 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 351 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 52 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 251 through 255 removed outlier: 3.740A pdb=" N ILE D 253 " --> pdb=" O HIS D 261 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N HIS D 261 " --> pdb=" O ILE D 253 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 972 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: 3.54 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8154 1.03 - 1.23: 1 1.23 - 1.42: 4189 1.42 - 1.61: 4839 1.61 - 1.81: 42 Bond restraints: 17225 Sorted by residual: bond pdb=" CB GLN C 296 " pdb=" CG GLN C 296 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.42e+00 bond pdb=" SD MET A 324 " pdb=" CE MET A 324 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 7.43e-01 bond pdb=" CA GLY D 3 " pdb=" C GLY D 3 " ideal model delta sigma weight residual 1.514 1.526 -0.012 1.41e-02 5.03e+03 7.31e-01 bond pdb=" CA MET D 1 " pdb=" CB MET D 1 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.52e-01 bond pdb=" CB GLU D 248 " pdb=" CG GLU D 248 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.50e-01 ... (remaining 17220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 29589 1.27 - 2.53: 980 2.53 - 3.80: 62 3.80 - 5.06: 7 5.06 - 6.33: 2 Bond angle restraints: 30640 Sorted by residual: angle pdb=" C THR D 247 " pdb=" N GLU D 248 " pdb=" CA GLU D 248 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CB GLN D 233 " pdb=" CG GLN D 233 " pdb=" CD GLN D 233 " ideal model delta sigma weight residual 112.60 117.57 -4.97 1.70e+00 3.46e-01 8.53e+00 angle pdb=" CA GLN C 296 " pdb=" CB GLN C 296 " pdb=" CG GLN C 296 " ideal model delta sigma weight residual 114.10 119.09 -4.99 2.00e+00 2.50e-01 6.23e+00 angle pdb=" N GLY A 109 " pdb=" CA GLY A 109 " pdb=" C GLY A 109 " ideal model delta sigma weight residual 112.04 114.41 -2.37 1.02e+00 9.61e-01 5.38e+00 angle pdb=" CB GLN C 296 " pdb=" CG GLN C 296 " pdb=" CD GLN C 296 " ideal model delta sigma weight residual 112.60 115.96 -3.36 1.70e+00 3.46e-01 3.91e+00 ... (remaining 30635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7177 17.79 - 35.57: 727 35.57 - 53.36: 228 53.36 - 71.15: 77 71.15 - 88.93: 20 Dihedral angle restraints: 8229 sinusoidal: 4220 harmonic: 4009 Sorted by residual: dihedral pdb=" CA GLU D 248 " pdb=" C GLU D 248 " pdb=" N LYS D 249 " pdb=" CA LYS D 249 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN B 68 " pdb=" C GLN B 68 " pdb=" N ILE B 69 " pdb=" CA ILE B 69 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP A 317 " pdb=" C TRP A 317 " pdb=" N TYR A 318 " pdb=" CA TYR A 318 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 8226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 668 0.029 - 0.059: 420 0.059 - 0.088: 87 0.088 - 0.117: 44 0.117 - 0.147: 14 Chirality restraints: 1233 Sorted by residual: chirality pdb=" CA VAL B 326 " pdb=" N VAL B 326 " pdb=" C VAL B 326 " pdb=" CB VAL B 326 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE C 356 " pdb=" N ILE C 356 " pdb=" C ILE C 356 " pdb=" CB ILE C 356 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA VAL B 288 " pdb=" N VAL B 288 " pdb=" C VAL B 288 " pdb=" CB VAL B 288 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1230 not shown) Planarity restraints: 2754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 282 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 283 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 282 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO C 283 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 267 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO D 268 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 268 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 268 " 0.016 5.00e-02 4.00e+02 ... (remaining 2751 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 388 2.08 - 2.71: 27605 2.71 - 3.34: 45703 3.34 - 3.97: 58845 3.97 - 4.60: 93124 Nonbonded interactions: 225665 Sorted by model distance: nonbonded pdb=" OE1 GLU A 124 " pdb=" HE1 TRP A 138 " model vdw 1.452 2.450 nonbonded pdb="HH11 ARG C 115 " pdb=" OD1 ASN C 150 " model vdw 1.557 2.450 nonbonded pdb=" O TYR C 117 " pdb="HE21 GLN C 172 " model vdw 1.577 2.450 nonbonded pdb="HH22 ARG C 148 " pdb=" OE2 GLU D 111 " model vdw 1.601 2.450 nonbonded pdb=" H PHE C 199 " pdb=" O ILE C 203 " model vdw 1.617 2.450 ... (remaining 225660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 44 through 46 or (resid 47 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 51 through 159 or (resid 160 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 164 thro \ ugh 302 or resid 305 through 360)) selection = (chain 'B' and (resid 23 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 44 through 46 or (resid 47 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 51 through 335 or resid 338 through 360)) selection = (chain 'C' and (resid 23 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or resi \ d 44 through 47 or resid 51 through 159 or (resid 160 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 164 through 302 or \ resid 305 through 335 or resid 338 through 360)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.250 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.003 0.036 9071 Z= 0.126 Angle : 0.547 6.326 12269 Z= 0.316 Chirality : 0.041 0.147 1233 Planarity : 0.003 0.043 1640 Dihedral : 16.308 86.903 3160 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.64 % Favored : 93.09 % Rotamer: Outliers : 2.05 % Allowed : 24.32 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1114 helix: -1.11 (0.48), residues: 103 sheet: 0.06 (0.22), residues: 527 loop : -2.29 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 115 TYR 0.018 0.001 TYR C 251 PHE 0.014 0.001 PHE B 100 TRP 0.012 0.001 TRP A 230 HIS 0.004 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 9071) covalent geometry : angle 0.54684 / 0.32 (12269) hydrogen bonds : bond 0.12872 / 8.70 ( 356) hydrogen bonds : angle 5.93202 / 4.02 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.489 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 138 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.6499 (p-90) REVERT: A 251 TYR cc_start: 0.6854 (t80) cc_final: 0.6601 (t80) REVERT: B 307 ASP cc_start: 0.8087 (p0) cc_final: 0.7359 (p0) REVERT: C 180 ASP cc_start: 0.8503 (m-30) cc_final: 0.8121 (t70) REVERT: C 257 ASN cc_start: 0.8566 (t0) cc_final: 0.8291 (t0) outliers start: 18 outliers final: 15 residues processed: 135 average time/residue: 0.1662 time to fit residues: 33.7484 Evaluate side-chains 130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 323 ASN ** C 249 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 = 0.3880 r_free = 0.3880 target = 0.150339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.117155 restraints weight = 40178.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122101 restraints weight = 17014.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125169 restraints weight = 10342.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126949 restraints weight = 7737.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128158 restraints weight = 6532.969| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9071 Z= 0.186 Angle : 0.538 5.343 12269 Z= 0.308 Chirality : 0.041 0.149 1233 Planarity : 0.004 0.047 1640 Dihedral : 6.372 56.043 1285 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.55 % Favored : 93.27 % Rotamer: Outliers : 4.20 % Allowed : 22.95 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.24), residues: 1114 helix: -1.13 (0.46), residues: 102 sheet: -0.14 (0.22), residues: 533 loop : -2.30 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 342 TYR 0.015 0.001 TYR A 318 PHE 0.011 0.001 PHE B 332 TRP 0.012 0.001 TRP B 230 HIS 0.008 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 ( 9071) covalent geometry : angle 0.53808 / 0.31 (12269) hydrogen bonds : bond 0.04285 / 2.99 ( 356) hydrogen bonds : angle 5.46206 / 3.67 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.483 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: B 282 ARG cc_start: 0.7202 (ttp-170) cc_final: 0.6542 (ttm-80) REVERT: C 256 GLU cc_start: 0.7860 (tp30) cc_final: 0.7078 (mp0) REVERT: C 257 ASN cc_start: 0.8617 (t0) cc_final: 0.8072 (t0) REVERT: C 317 TRP cc_start: 0.8427 (OUTLIER) cc_final: 0.8206 (m-10) outliers start: 37 outliers final: 30 residues processed: 146 average time/residue: 0.1634 time to fit residues: 36.2102 Evaluate side-chains 140 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 317 TRP Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112316 restraints weight = 40537.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.117197 restraints weight = 17139.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120225 restraints weight = 10398.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122076 restraints weight = 7775.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123057 restraints weight = 6559.289| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9071 Z= 0.233 Angle : 0.557 5.828 12269 Z= 0.318 Chirality : 0.041 0.151 1233 Planarity : 0.003 0.045 1640 Dihedral : 6.377 58.398 1276 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.81 % Favored : 92.01 % Rotamer: Outliers : 5.34 % Allowed : 21.93 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.24), residues: 1114 helix: -1.17 (0.46), residues: 106 sheet: -0.34 (0.22), residues: 533 loop : -2.43 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 181 TYR 0.017 0.002 TYR B 327 PHE 0.016 0.002 PHE B 332 TRP 0.014 0.001 TRP B 230 HIS 0.006 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 ( 9071) covalent geometry : angle 0.55694 / 0.32 (12269) hydrogen bonds : bond 0.04334 / 3.00 ( 356) hydrogen bonds : angle 5.38000 / 3.60 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 0.507 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: B 268 ASN cc_start: 0.8490 (m-40) cc_final: 0.8100 (m-40) REVERT: B 282 ARG cc_start: 0.7508 (ttp-170) cc_final: 0.6667 (ttm-80) outliers start: 47 outliers final: 38 residues processed: 149 average time/residue: 0.1605 time to fit residues: 36.5281 Evaluate side-chains 142 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 GLN ** C 249 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 = 0.3825 r_free = 0.3825 target = 0.145974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112258 restraints weight = 40048.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117198 restraints weight = 16671.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120176 restraints weight = 9980.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122074 restraints weight = 7456.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123229 restraints weight = 6230.396| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9071 Z= 0.185 Angle : 0.516 5.111 12269 Z= 0.295 Chirality : 0.040 0.148 1233 Planarity : 0.003 0.045 1640 Dihedral : 5.814 55.798 1270 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.18 % Favored : 92.64 % Rotamer: Outliers : 4.66 % Allowed : 22.39 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.24), residues: 1114 helix: -0.99 (0.48), residues: 105 sheet: -0.33 (0.22), residues: 534 loop : -2.39 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.018 0.001 TYR A 251 PHE 0.014 0.001 PHE B 332 TRP 0.014 0.001 TRP B 230 HIS 0.005 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 9071) covalent geometry : angle 0.51631 / 0.30 (12269) hydrogen bonds : bond 0.03720 / 2.58 ( 356) hydrogen bonds : angle 5.23158 / 3.50 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.489 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 324 MET cc_start: 0.7618 (tpt) cc_final: 0.7344 (tpt) REVERT: B 268 ASN cc_start: 0.8482 (m-40) cc_final: 0.8095 (m-40) outliers start: 41 outliers final: 29 residues processed: 149 average time/residue: 0.1692 time to fit residues: 38.2735 Evaluate side-chains 137 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 223 ASN ** C 249 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 = 0.3813 r_free = 0.3813 target = 0.144947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111120 restraints weight = 40562.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115901 restraints weight = 17331.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118882 restraints weight = 10567.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120445 restraints weight = 7903.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121675 restraints weight = 6774.205| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9071 Z= 0.231 Angle : 0.540 5.408 12269 Z= 0.309 Chirality : 0.040 0.148 1233 Planarity : 0.003 0.043 1640 Dihedral : 5.870 56.071 1266 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.35 % Favored : 91.47 % Rotamer: Outliers : 5.00 % Allowed : 21.59 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.24), residues: 1114 helix: -0.92 (0.48), residues: 107 sheet: -0.46 (0.22), residues: 534 loop : -2.34 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 298 TYR 0.018 0.002 TYR A 318 PHE 0.016 0.002 PHE B 332 TRP 0.013 0.001 TRP B 230 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.23 ( 9071) covalent geometry : angle 0.54037 / 0.31 (12269) hydrogen bonds : bond 0.03919 / 2.72 ( 356) hydrogen bonds : angle 5.26233 / 3.53 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.506 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: A 324 MET cc_start: 0.7649 (tpt) cc_final: 0.7333 (tpt) REVERT: A 349 ASP cc_start: 0.7009 (p0) cc_final: 0.6342 (p0) REVERT: B 268 ASN cc_start: 0.8537 (m-40) cc_final: 0.8161 (m-40) outliers start: 44 outliers final: 34 residues processed: 147 average time/residue: 0.1714 time to fit residues: 37.9991 Evaluate side-chains 143 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110409 restraints weight = 40215.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115222 restraints weight = 16881.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118213 restraints weight = 10169.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120079 restraints weight = 7567.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.120990 restraints weight = 6342.681| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9071 Z= 0.211 Angle : 0.530 5.576 12269 Z= 0.302 Chirality : 0.040 0.146 1233 Planarity : 0.003 0.042 1640 Dihedral : 5.801 56.353 1264 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.36 % Favored : 92.46 % Rotamer: Outliers : 4.77 % Allowed : 22.27 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.25), residues: 1114 helix: -0.77 (0.48), residues: 107 sheet: -0.49 (0.22), residues: 535 loop : -2.30 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.016 0.002 TYR A 318 PHE 0.017 0.002 PHE B 332 TRP 0.010 0.001 TRP B 230 HIS 0.005 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.21 ( 9071) covalent geometry : angle 0.52989 / 0.30 (12269) hydrogen bonds : bond 0.03701 / 2.56 ( 356) hydrogen bonds : angle 5.21504 / 3.50 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.501 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: A 160 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.5438 (t80) REVERT: A 349 ASP cc_start: 0.7016 (p0) cc_final: 0.6374 (p0) REVERT: B 268 ASN cc_start: 0.8525 (m-40) cc_final: 0.8175 (m-40) outliers start: 42 outliers final: 32 residues processed: 140 average time/residue: 0.1698 time to fit residues: 35.8237 Evaluate side-chains 139 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.142277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108569 restraints weight = 40929.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113303 restraints weight = 17323.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116245 restraints weight = 10506.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117853 restraints weight = 7831.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119006 restraints weight = 6677.217| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 9071 Z= 0.328 Angle : 0.601 5.619 12269 Z= 0.344 Chirality : 0.042 0.148 1233 Planarity : 0.003 0.044 1640 Dihedral : 6.101 56.387 1264 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.14 % Favored : 89.68 % Rotamer: Outliers : 6.02 % Allowed : 21.93 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.24), residues: 1114 helix: -0.76 (0.49), residues: 105 sheet: -0.77 (0.22), residues: 544 loop : -2.45 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.020 0.002 TYR B 327 PHE 0.022 0.002 PHE B 332 TRP 0.008 0.001 TRP B 317 HIS 0.006 0.002 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.33 ( 9071) covalent geometry : angle 0.60148 / 0.34 (12269) hydrogen bonds : bond 0.04343 / 3.01 ( 356) hydrogen bonds : angle 5.42590 / 3.65 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 0.493 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: A 136 ASP cc_start: 0.7667 (t0) cc_final: 0.7426 (t0) REVERT: A 160 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.5517 (t80) REVERT: A 349 ASP cc_start: 0.6988 (p0) cc_final: 0.6351 (p0) REVERT: B 268 ASN cc_start: 0.8610 (m-40) cc_final: 0.8248 (m-40) REVERT: D 110 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8026 (p0) outliers start: 53 outliers final: 44 residues processed: 145 average time/residue: 0.1672 time to fit residues: 36.6393 Evaluate side-chains 152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 187 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 275 TYR Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.145393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111598 restraints weight = 39928.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116488 restraints weight = 16759.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119514 restraints weight = 10101.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121393 restraints weight = 7491.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122324 restraints weight = 6268.305| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9071 Z= 0.126 Angle : 0.513 6.654 12269 Z= 0.292 Chirality : 0.040 0.152 1233 Planarity : 0.003 0.041 1640 Dihedral : 5.746 56.282 1264 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 3.64 % Allowed : 24.32 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.25), residues: 1114 helix: -0.64 (0.48), residues: 113 sheet: -0.52 (0.23), residues: 534 loop : -2.26 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 214 TYR 0.013 0.001 TYR A 318 PHE 0.013 0.001 PHE B 332 TRP 0.013 0.001 TRP A 230 HIS 0.005 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 9071) covalent geometry : angle 0.51334 / 0.29 (12269) hydrogen bonds : bond 0.03363 / 2.33 ( 356) hydrogen bonds : angle 5.19192 / 3.47 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.476 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: A 160 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.5421 (t80) REVERT: A 261 TYR cc_start: 0.8366 (m-80) cc_final: 0.8033 (m-80) REVERT: A 349 ASP cc_start: 0.6979 (p0) cc_final: 0.6371 (p0) REVERT: B 268 ASN cc_start: 0.8550 (m-40) cc_final: 0.8197 (m-40) outliers start: 32 outliers final: 28 residues processed: 136 average time/residue: 0.1693 time to fit residues: 34.7612 Evaluate side-chains 139 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 150 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113286 restraints weight = 39935.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118216 restraints weight = 16643.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121302 restraints weight = 9989.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123085 restraints weight = 7405.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124012 restraints weight = 6237.649| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9071 Z= 0.107 Angle : 0.481 6.904 12269 Z= 0.272 Chirality : 0.040 0.144 1233 Planarity : 0.003 0.042 1640 Dihedral : 5.414 55.708 1264 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 2.61 % Allowed : 25.23 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.25), residues: 1114 helix: -0.46 (0.48), residues: 113 sheet: -0.50 (0.23), residues: 546 loop : -2.05 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 214 TYR 0.012 0.001 TYR A 318 PHE 0.008 0.001 PHE B 332 TRP 0.013 0.001 TRP A 230 HIS 0.003 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9071) covalent geometry : angle 0.48064 / 0.27 (12269) hydrogen bonds : bond 0.02959 / 2.04 ( 356) hydrogen bonds : angle 4.94946 / 3.31 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.486 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: A 160 PHE cc_start: 0.6416 (OUTLIER) cc_final: 0.5286 (t80) REVERT: A 228 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: A 261 TYR cc_start: 0.8286 (m-80) cc_final: 0.7991 (m-80) REVERT: A 349 ASP cc_start: 0.6877 (p0) cc_final: 0.6268 (p0) REVERT: B 268 ASN cc_start: 0.8547 (m-40) cc_final: 0.8206 (m-40) REVERT: D 101 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.4789 (pt0) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 0.1743 time to fit residues: 33.1861 Evaluate side-chains 130 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112418 restraints weight = 40106.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.117275 restraints weight = 17207.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120243 restraints weight = 10490.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121808 restraints weight = 7867.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.123080 restraints weight = 6743.159| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9071 Z= 0.162 Angle : 0.499 6.599 12269 Z= 0.284 Chirality : 0.040 0.146 1233 Planarity : 0.003 0.038 1640 Dihedral : 5.427 55.980 1261 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.28 % Favored : 93.54 % Rotamer: Outliers : 2.27 % Allowed : 26.02 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.25), residues: 1114 helix: -0.41 (0.48), residues: 113 sheet: -0.52 (0.23), residues: 546 loop : -2.07 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 97 TYR 0.016 0.001 TYR A 318 PHE 0.013 0.001 PHE B 332 TRP 0.010 0.001 TRP A 230 HIS 0.003 0.001 HIS C 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 9071) covalent geometry : angle 0.49902 / 0.28 (12269) hydrogen bonds : bond 0.03259 / 2.25 ( 356) hydrogen bonds : angle 4.97266 / 3.32 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 47 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.493 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: A 160 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5342 (t80) REVERT: A 228 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: A 261 TYR cc_start: 0.8321 (m-80) cc_final: 0.8026 (m-80) REVERT: A 349 ASP cc_start: 0.6883 (p0) cc_final: 0.6281 (p0) REVERT: B 268 ASN cc_start: 0.8561 (m-40) cc_final: 0.8230 (m-40) REVERT: D 101 GLU cc_start: 0.5391 (OUTLIER) cc_final: 0.4813 (pt0) outliers start: 20 outliers final: 17 residues processed: 127 average time/residue: 0.1780 time to fit residues: 33.6506 Evaluate side-chains 131 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 191 PHE Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 6 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.0191 > 50:) chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.114167 restraints weight = 39699.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119093 restraints weight = 16767.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.122075 restraints weight = 10106.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123968 restraints weight = 7548.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125109 restraints weight = 6315.417| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9071 Z= 0.095 Angle : 0.473 7.002 12269 Z= 0.268 Chirality : 0.040 0.146 1233 Planarity : 0.003 0.041 1640 Dihedral : 5.228 55.509 1261 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.39 % Favored : 94.43 % Rotamer: Outliers : 1.93 % Allowed : 26.48 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.25), residues: 1114 helix: -0.29 (0.49), residues: 113 sheet: -0.34 (0.23), residues: 544 loop : -1.99 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 298 TYR 0.011 0.001 TYR C 275 PHE 0.008 0.001 PHE B 332 TRP 0.012 0.001 TRP A 230 HIS 0.003 0.001 HIS D 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 ( 9071) covalent geometry : angle 0.47321 / 0.27 (12269) hydrogen bonds : bond 0.02805 / 1.93 ( 356) hydrogen bonds : angle 4.83408 / 3.22 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.63 seconds wall clock time: 55 minutes 38.81 seconds (3338.81 seconds total)