Starting phenix.real_space_refine on Thu Jul 2 12:42:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jei_36189/07_2026/8jei_36189_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jei_36189/07_2026/8jei_36189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jei_36189/07_2026/8jei_36189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jei_36189/07_2026/8jei_36189.map" model { file = "/net/cci-nas-00/data/ceres_data/8jei_36189/07_2026/8jei_36189_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jei_36189/07_2026/8jei_36189_neut.cif" } resolution = 2.73 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= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5577 2.51 5 N 1485 2.21 5 O 1598 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1710 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2219 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 9, 'TRANS': 275} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 2, 'PHE:plan': 4, 'GLN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'CW3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.49, per 1000 atoms: 0.17 Number of scatterers: 8725 At special positions: 0 Unit cell: (87.98, 119.52, 127.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1598 8.00 N 1485 7.00 C 5577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 417.7 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 37.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 6 through 32 removed outlier: 3.504A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.469A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 216 " --> pdb=" O HIS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.579A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.520A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 310 Processing helix chain 'C' and resid 330 through 352 Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.854A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.511A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.104A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.761A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 41 removed outlier: 4.040A pdb=" N ALA A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 60 through 89 Proline residue: A 81 - end of helix removed outlier: 3.672A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 131 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.708A pdb=" N ILE A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 165 removed outlier: 5.121A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 6.129A pdb=" N PHE A 193 " --> pdb=" O HIS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 218 removed outlier: 3.676A pdb=" N ARG A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 261 removed outlier: 3.519A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 269 through 294 removed outlier: 3.575A pdb=" N ASP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.600A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.559A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.265A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.362A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.500A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.373A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.601A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.069A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.534A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1260 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: 1.24 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2288 1.33 - 1.45: 1731 1.45 - 1.57: 4803 1.57 - 1.69: 2 1.69 - 1.81: 93 Bond restraints: 8917 Sorted by residual: bond pdb=" ND1 HIS A 131 " pdb=" CE1 HIS A 131 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.82e+01 bond pdb=" ND1 HIS A 223 " pdb=" CE1 HIS A 223 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.75e+01 bond pdb=" ND1 HIS A 253 " pdb=" CE1 HIS A 253 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.69e+01 bond pdb=" CD GLN A 217 " pdb=" OE1 GLN A 217 " ideal model delta sigma weight residual 1.231 1.329 -0.098 1.90e-02 2.77e+03 2.64e+01 bond pdb=" CG ASN A 110 " pdb=" OD1 ASN A 110 " ideal model delta sigma weight residual 1.231 1.328 -0.097 1.90e-02 2.77e+03 2.63e+01 ... (remaining 8912 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 12022 5.11 - 10.22: 48 10.22 - 15.33: 8 15.33 - 20.44: 6 20.44 - 25.55: 5 Bond angle restraints: 12089 Sorted by residual: angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 110.68 135.05 -24.37 1.39e+00 5.18e-01 3.07e+02 angle pdb=" N ALA C 300 " pdb=" CA ALA C 300 " pdb=" C ALA C 300 " ideal model delta sigma weight residual 111.02 85.47 25.55 1.52e+00 4.33e-01 2.82e+02 angle pdb=" N ALA C 299 " pdb=" CA ALA C 299 " pdb=" C ALA C 299 " ideal model delta sigma weight residual 113.28 138.57 -25.29 1.57e+00 4.06e-01 2.59e+02 angle pdb=" C ARG A 22 " pdb=" CA ARG A 22 " pdb=" CB ARG A 22 " ideal model delta sigma weight residual 111.50 87.16 24.34 1.64e+00 3.72e-01 2.20e+02 angle pdb=" N CYS A 18 " pdb=" CA CYS A 18 " pdb=" C CYS A 18 " ideal model delta sigma weight residual 108.52 128.93 -20.41 1.52e+00 4.33e-01 1.80e+02 ... (remaining 12084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4768 17.57 - 35.13: 387 35.13 - 52.70: 74 52.70 - 70.26: 12 70.26 - 87.83: 9 Dihedral angle restraints: 5250 sinusoidal: 1989 harmonic: 3261 Sorted by residual: dihedral pdb=" C ARG A 22 " pdb=" N ARG A 22 " pdb=" CA ARG A 22 " pdb=" CB ARG A 22 " ideal model delta harmonic sigma weight residual -122.60 -91.38 -31.22 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N ALA C 300 " pdb=" C ALA C 300 " pdb=" CA ALA C 300 " pdb=" CB ALA C 300 " ideal model delta harmonic sigma weight residual 122.90 92.36 30.54 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N ASP A 23 " pdb=" C ASP A 23 " pdb=" CA ASP A 23 " pdb=" CB ASP A 23 " ideal model delta harmonic sigma weight residual 122.80 97.30 25.50 0 2.50e+00 1.60e-01 1.04e+02 ... (remaining 5247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 1351 0.169 - 0.337: 9 0.337 - 0.506: 7 0.506 - 0.674: 4 0.674 - 0.843: 1 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA ALA C 299 " pdb=" N ALA C 299 " pdb=" C ALA C 299 " pdb=" CB ALA C 299 " both_signs ideal model delta sigma weight residual False 2.48 1.64 0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb=" CA ARG A 22 " pdb=" N ARG A 22 " pdb=" C ARG A 22 " pdb=" CB ARG A 22 " both_signs ideal model delta sigma weight residual False 2.51 3.13 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" CA CYS A 19 " pdb=" N CYS A 19 " pdb=" C CYS A 19 " pdb=" CB CYS A 19 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.52e+00 ... (remaining 1369 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " -0.192 2.00e-02 2.50e+03 1.03e-01 2.13e+02 pdb=" CG TYR A 284 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " 0.092 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " 0.080 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 93 " 0.102 2.00e-02 2.50e+03 5.90e-02 8.72e+01 pdb=" CG TRP A 93 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 93 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 93 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A 93 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP A 93 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 93 " -0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 93 " 0.073 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 93 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP A 93 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 CW3 A 401 " 0.024 2.00e-02 2.50e+03 4.33e-02 4.22e+01 pdb=" C06 CW3 A 401 " -0.017 2.00e-02 2.50e+03 pdb=" C07 CW3 A 401 " -0.075 2.00e-02 2.50e+03 pdb=" C08 CW3 A 401 " -0.012 2.00e-02 2.50e+03 pdb=" C09 CW3 A 401 " 0.009 2.00e-02 2.50e+03 pdb=" C10 CW3 A 401 " 0.020 2.00e-02 2.50e+03 pdb=" C14 CW3 A 401 " 0.058 2.00e-02 2.50e+03 pdb=" N04 CW3 A 401 " 0.053 2.00e-02 2.50e+03 pdb=" N11 CW3 A 401 " -0.061 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 194 2.69 - 3.24: 8448 3.24 - 3.79: 13998 3.79 - 4.35: 18861 4.35 - 4.90: 31842 Nonbonded interactions: 73343 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.132 3.040 nonbonded pdb=" O ARG A 22 " pdb=" CB ARG A 22 " model vdw 2.137 2.752 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.163 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.171 3.040 nonbonded pdb=" O HIS A 184 " pdb=" O THR A 185 " model vdw 2.173 3.040 ... (remaining 73338 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 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 : 0.005 0.115 8922 Z= 0.323 Angle : 1.055 25.547 12099 Z= 0.663 Chirality : 0.069 0.843 1372 Planarity : 0.006 0.103 1526 Dihedral : 13.429 83.327 3129 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.69 % Favored : 95.13 % Rotamer: Outliers : 1.51 % Allowed : 1.40 % Favored : 97.08 % Cbeta Deviations : 0.85 % 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: 0.03 (0.26), residues: 1109 helix: 1.36 (0.28), residues: 369 sheet: -0.32 (0.29), residues: 276 loop : -0.78 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 89 TYR 0.192 0.005 TYR A 284 PHE 0.035 0.002 PHE A 180 TRP 0.102 0.004 TRP A 93 HIS 0.015 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.32 ( 8917) covalent geometry : angle 1.05492 / 0.66 (12089) SS BOND : bond 0.00290 / 0.14 ( 5) SS BOND : angle 1.57803 / 0.91 ( 10) hydrogen bonds : bond 0.13360 / 8.88 ( 450) hydrogen bonds : angle 5.84873 / 4.15 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.336 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 349 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8161 (mtpp) REVERT: A 45 ASN cc_start: 0.8089 (m-40) cc_final: 0.7825 (m110) REVERT: A 74 PHE cc_start: 0.8243 (t80) cc_final: 0.8015 (t80) REVERT: A 83 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8423 (p) REVERT: A 149 CYS cc_start: 0.8017 (m) cc_final: 0.7424 (m) REVERT: A 216 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7754 (ptp-110) REVERT: A 222 ARG cc_start: 0.7627 (mpt-90) cc_final: 0.7417 (ptt180) REVERT: A 285 MET cc_start: 0.8619 (mtp) cc_final: 0.8118 (mtm) outliers start: 14 outliers final: 6 residues processed: 186 average time/residue: 0.4809 time to fit residues: 95.3017 Evaluate side-chains 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN B 237 ASN A 110 ASN A 253 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.080680 restraints weight = 11793.082| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.79 r_work: 0.2798 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8922 Z= 0.242 Angle : 0.626 8.901 12099 Z= 0.336 Chirality : 0.046 0.290 1372 Planarity : 0.004 0.053 1526 Dihedral : 5.732 50.814 1227 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 2.92 % Allowed : 10.80 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.35 (0.26), residues: 1109 helix: 1.78 (0.27), residues: 374 sheet: -0.34 (0.28), residues: 284 loop : -0.64 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.041 0.002 TYR S 235 PHE 0.022 0.002 PHE C 274 TRP 0.021 0.002 TRP A 188 HIS 0.007 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 ( 8917) covalent geometry : angle 0.62603 / 0.34 (12089) SS BOND : bond 0.00381 / 0.20 ( 5) SS BOND : angle 1.04533 / 0.59 ( 10) hydrogen bonds : bond 0.04168 / 2.74 ( 450) hydrogen bonds : angle 4.78061 / 3.44 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.351 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 349 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7862 (mtpp) REVERT: B 13 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (pp30) REVERT: B 217 MET cc_start: 0.8352 (ptt) cc_final: 0.7989 (pmm) REVERT: S 186 GLN cc_start: 0.8505 (tt0) cc_final: 0.8302 (tt0) REVERT: A 45 ASN cc_start: 0.8153 (m-40) cc_final: 0.7679 (m110) REVERT: A 74 PHE cc_start: 0.8263 (t80) cc_final: 0.7971 (t80) REVERT: A 149 CYS cc_start: 0.7948 (m) cc_final: 0.7476 (m) REVERT: A 222 ARG cc_start: 0.8030 (mpt-90) cc_final: 0.7500 (ptt180) REVERT: A 234 MET cc_start: 0.8053 (mmm) cc_final: 0.7405 (mtt) REVERT: A 273 ASP cc_start: 0.8601 (t0) cc_final: 0.8356 (t0) REVERT: A 287 SER cc_start: 0.8354 (m) cc_final: 0.8129 (p) outliers start: 27 outliers final: 9 residues processed: 162 average time/residue: 0.5340 time to fit residues: 92.1079 Evaluate side-chains 149 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN B 16 ASN B 237 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.082879 restraints weight = 11578.326| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.77 r_work: 0.2792 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8922 Z= 0.142 Angle : 0.548 7.281 12099 Z= 0.295 Chirality : 0.044 0.216 1372 Planarity : 0.004 0.058 1526 Dihedral : 5.159 44.143 1223 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.40 % Rotamer: Outliers : 2.59 % Allowed : 13.82 % Favored : 83.59 % 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: 0.42 (0.26), residues: 1109 helix: 1.93 (0.27), residues: 374 sheet: -0.33 (0.29), residues: 278 loop : -0.67 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 160 TYR 0.033 0.002 TYR S 235 PHE 0.016 0.001 PHE A 232 TRP 0.018 0.001 TRP A 188 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8917) covalent geometry : angle 0.54731 / 0.30 (12089) SS BOND : bond 0.00333 / 0.18 ( 5) SS BOND : angle 0.92518 / 0.52 ( 10) hydrogen bonds : bond 0.03643 / 2.42 ( 450) hydrogen bonds : angle 4.59452 / 3.33 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.261 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (m-30) REVERT: C 313 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7229 (ptm160) REVERT: C 349 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7862 (ttmm) REVERT: B 13 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8058 (pp30) REVERT: B 217 MET cc_start: 0.8344 (ptt) cc_final: 0.7927 (pmm) REVERT: B 274 THR cc_start: 0.9262 (p) cc_final: 0.8995 (p) REVERT: A 20 VAL cc_start: 0.8447 (m) cc_final: 0.8217 (t) REVERT: A 45 ASN cc_start: 0.8255 (m-40) cc_final: 0.7666 (m110) REVERT: A 68 ASN cc_start: 0.8123 (m110) cc_final: 0.7890 (m-40) REVERT: A 74 PHE cc_start: 0.8202 (t80) cc_final: 0.7918 (t80) REVERT: A 149 CYS cc_start: 0.7913 (m) cc_final: 0.7407 (m) REVERT: A 222 ARG cc_start: 0.8027 (mpt-90) cc_final: 0.7430 (ptt180) REVERT: A 234 MET cc_start: 0.8087 (mmm) cc_final: 0.7448 (mtt) REVERT: A 287 SER cc_start: 0.8462 (m) cc_final: 0.8243 (p) outliers start: 24 outliers final: 10 residues processed: 160 average time/residue: 0.5696 time to fit residues: 96.5521 Evaluate side-chains 156 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 282 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN B 237 ASN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.078926 restraints weight = 11823.390| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.78 r_work: 0.2729 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 8922 Z= 0.273 Angle : 0.610 7.231 12099 Z= 0.329 Chirality : 0.046 0.265 1372 Planarity : 0.004 0.058 1526 Dihedral : 5.202 41.752 1223 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.13 % Allowed : 15.01 % Favored : 81.86 % 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: 0.33 (0.25), residues: 1109 helix: 1.92 (0.27), residues: 368 sheet: -0.36 (0.28), residues: 283 loop : -0.76 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 160 TYR 0.038 0.002 TYR S 235 PHE 0.014 0.002 PHE A 197 TRP 0.022 0.002 TRP A 188 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.27 ( 8917) covalent geometry : angle 0.60922 / 0.33 (12089) SS BOND : bond 0.00501 / 0.25 ( 5) SS BOND : angle 1.12151 / 0.60 ( 10) hydrogen bonds : bond 0.04090 / 2.70 ( 450) hydrogen bonds : angle 4.76242 / 3.45 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.358 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: C 21 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6370 (ttp80) REVERT: C 279 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8574 (mtmm) REVERT: C 305 CYS cc_start: 0.8336 (m) cc_final: 0.7919 (m) REVERT: C 313 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7314 (ptm160) REVERT: C 349 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7879 (ttmm) REVERT: B 13 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8064 (pp30) REVERT: B 23 LYS cc_start: 0.8404 (mmmm) cc_final: 0.8137 (ttmm) REVERT: B 217 MET cc_start: 0.8236 (ptt) cc_final: 0.7835 (pmt) REVERT: G 48 ASP cc_start: 0.8996 (t0) cc_final: 0.8704 (t0) REVERT: S 235 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6554 (t80) REVERT: A 20 VAL cc_start: 0.8478 (m) cc_final: 0.8219 (t) REVERT: A 45 ASN cc_start: 0.8372 (m-40) cc_final: 0.7763 (m110) REVERT: A 68 ASN cc_start: 0.8270 (m110) cc_final: 0.7997 (m-40) REVERT: A 74 PHE cc_start: 0.8210 (t80) cc_final: 0.7940 (t80) REVERT: A 149 CYS cc_start: 0.8016 (m) cc_final: 0.7524 (m) REVERT: A 222 ARG cc_start: 0.8064 (mpt-90) cc_final: 0.7502 (ptt180) REVERT: A 277 PHE cc_start: 0.8074 (m-80) cc_final: 0.7399 (m-80) REVERT: A 287 SER cc_start: 0.8545 (m) cc_final: 0.8318 (p) outliers start: 29 outliers final: 13 residues processed: 149 average time/residue: 0.5601 time to fit residues: 88.4210 Evaluate side-chains 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN B 16 ASN ** A 286 ASN ** 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 = 0.3629 r_free = 0.3629 target = 0.131110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.081816 restraints weight = 11753.762| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.79 r_work: 0.2805 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8922 Z= 0.144 Angle : 0.547 9.385 12099 Z= 0.293 Chirality : 0.043 0.200 1372 Planarity : 0.004 0.058 1526 Dihedral : 4.675 34.790 1219 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 2.92 % Allowed : 16.41 % Favored : 80.67 % 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: 0.49 (0.25), residues: 1109 helix: 2.19 (0.28), residues: 358 sheet: -0.31 (0.28), residues: 282 loop : -0.70 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.034 0.001 TYR S 235 PHE 0.010 0.001 PHE B 199 TRP 0.022 0.001 TRP A 188 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8917) covalent geometry : angle 0.54682 / 0.29 (12089) SS BOND : bond 0.00392 / 0.21 ( 5) SS BOND : angle 0.76926 / 0.41 ( 10) hydrogen bonds : bond 0.03556 / 2.37 ( 450) hydrogen bonds : angle 4.59596 / 3.33 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.297 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7964 (m-30) REVERT: C 21 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6369 (ttp80) REVERT: C 305 CYS cc_start: 0.8272 (m) cc_final: 0.7837 (m) REVERT: C 349 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7891 (ttmm) REVERT: B 13 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8065 (pp30) REVERT: B 23 LYS cc_start: 0.8426 (mmmm) cc_final: 0.8193 (ttmm) REVERT: B 217 MET cc_start: 0.8262 (ptt) cc_final: 0.7931 (pmt) REVERT: B 274 THR cc_start: 0.9242 (p) cc_final: 0.9026 (p) REVERT: G 48 ASP cc_start: 0.8983 (t0) cc_final: 0.8740 (t0) REVERT: S 186 GLN cc_start: 0.8360 (tt0) cc_final: 0.8123 (pt0) REVERT: S 235 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6246 (t80) REVERT: A 45 ASN cc_start: 0.8338 (m-40) cc_final: 0.7904 (m-40) REVERT: A 68 ASN cc_start: 0.8248 (m110) cc_final: 0.7992 (m-40) REVERT: A 74 PHE cc_start: 0.8165 (t80) cc_final: 0.7869 (t80) REVERT: A 149 CYS cc_start: 0.7984 (m) cc_final: 0.7472 (m) REVERT: A 192 MET cc_start: 0.6222 (mpt) cc_final: 0.6020 (mpt) REVERT: A 216 ARG cc_start: 0.7820 (ptp-110) cc_final: 0.7606 (ptp-110) REVERT: A 222 ARG cc_start: 0.8012 (mpt-90) cc_final: 0.7431 (ptt180) REVERT: A 234 MET cc_start: 0.8068 (mmm) cc_final: 0.7440 (mtt) REVERT: A 277 PHE cc_start: 0.8081 (m-80) cc_final: 0.7346 (m-80) REVERT: A 287 SER cc_start: 0.8552 (m) cc_final: 0.8305 (p) outliers start: 27 outliers final: 10 residues processed: 163 average time/residue: 0.4941 time to fit residues: 85.6951 Evaluate side-chains 157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.0010 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN B 16 ASN B 237 ASN A 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.082852 restraints weight = 11557.539| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.78 r_work: 0.2833 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8922 Z= 0.125 Angle : 0.537 7.943 12099 Z= 0.287 Chirality : 0.043 0.186 1372 Planarity : 0.004 0.058 1526 Dihedral : 4.518 32.685 1219 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.38 % Allowed : 18.25 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.26), residues: 1109 helix: 2.26 (0.28), residues: 358 sheet: -0.30 (0.29), residues: 277 loop : -0.69 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 160 TYR 0.032 0.001 TYR S 235 PHE 0.013 0.001 PHE A 232 TRP 0.020 0.001 TRP A 188 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8917) covalent geometry : angle 0.53698 / 0.29 (12089) SS BOND : bond 0.00361 / 0.19 ( 5) SS BOND : angle 0.73804 / 0.40 ( 10) hydrogen bonds : bond 0.03402 / 2.26 ( 450) hydrogen bonds : angle 4.49902 / 3.27 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.257 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: C 205 ARG cc_start: 0.8459 (mmp80) cc_final: 0.8159 (mmp80) REVERT: C 305 CYS cc_start: 0.8182 (m) cc_final: 0.7780 (m) REVERT: C 349 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7832 (ttmm) REVERT: B 13 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8063 (pp30) REVERT: B 23 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8103 (ttmm) REVERT: B 217 MET cc_start: 0.8163 (ptt) cc_final: 0.7765 (pmt) REVERT: B 274 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8956 (p) REVERT: G 48 ASP cc_start: 0.8878 (t0) cc_final: 0.8651 (t0) REVERT: S 186 GLN cc_start: 0.8245 (tt0) cc_final: 0.7972 (pt0) REVERT: S 235 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6194 (t80) REVERT: A 45 ASN cc_start: 0.8319 (m-40) cc_final: 0.7859 (m-40) REVERT: A 68 ASN cc_start: 0.8106 (m110) cc_final: 0.7849 (m-40) REVERT: A 74 PHE cc_start: 0.8169 (t80) cc_final: 0.7877 (t80) REVERT: A 93 TRP cc_start: 0.7404 (t-100) cc_final: 0.7123 (t-100) REVERT: A 149 CYS cc_start: 0.7934 (m) cc_final: 0.7418 (m) REVERT: A 192 MET cc_start: 0.6326 (OUTLIER) cc_final: 0.6120 (mpt) REVERT: A 216 ARG cc_start: 0.7818 (ptp-110) cc_final: 0.7586 (ptp-110) REVERT: A 222 ARG cc_start: 0.8043 (mpt-90) cc_final: 0.7429 (ptt180) REVERT: A 234 MET cc_start: 0.8068 (mmm) cc_final: 0.7440 (mtt) REVERT: A 273 ASP cc_start: 0.8523 (t0) cc_final: 0.8088 (t0) REVERT: A 277 PHE cc_start: 0.8001 (m-80) cc_final: 0.7405 (m-80) outliers start: 22 outliers final: 12 residues processed: 158 average time/residue: 0.4935 time to fit residues: 83.0323 Evaluate side-chains 157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.082148 restraints weight = 11708.592| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.86 r_work: 0.2790 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8922 Z= 0.133 Angle : 0.540 7.749 12099 Z= 0.288 Chirality : 0.043 0.186 1372 Planarity : 0.004 0.058 1526 Dihedral : 4.450 31.586 1218 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.92 % Allowed : 18.25 % Favored : 78.83 % 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: 0.54 (0.26), residues: 1109 helix: 2.27 (0.28), residues: 358 sheet: -0.27 (0.29), residues: 277 loop : -0.71 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG S 160 TYR 0.033 0.001 TYR S 235 PHE 0.011 0.001 PHE A 232 TRP 0.018 0.001 TRP A 188 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 8917) covalent geometry : angle 0.54008 / 0.29 (12089) SS BOND : bond 0.00362 / 0.19 ( 5) SS BOND : angle 0.77473 / 0.42 ( 10) hydrogen bonds : bond 0.03385 / 2.25 ( 450) hydrogen bonds : angle 4.48566 / 3.25 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.239 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: C 20 ASP cc_start: 0.8371 (m-30) cc_final: 0.8130 (m-30) REVERT: C 21 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6276 (ttp80) REVERT: C 276 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8654 (mm-30) REVERT: C 305 CYS cc_start: 0.8200 (m) cc_final: 0.7815 (m) REVERT: C 349 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7825 (ttmm) REVERT: B 13 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8051 (pp30) REVERT: B 23 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8100 (ttmm) REVERT: B 217 MET cc_start: 0.8198 (ptt) cc_final: 0.7759 (pmt) REVERT: B 258 ASP cc_start: 0.8355 (t70) cc_final: 0.7732 (t0) REVERT: G 48 ASP cc_start: 0.8846 (t0) cc_final: 0.8575 (t0) REVERT: S 186 GLN cc_start: 0.8261 (tt0) cc_final: 0.7975 (pt0) REVERT: S 235 TYR cc_start: 0.7104 (OUTLIER) cc_final: 0.6265 (t80) REVERT: A 45 ASN cc_start: 0.8322 (m-40) cc_final: 0.7879 (m-40) REVERT: A 68 ASN cc_start: 0.8132 (m110) cc_final: 0.7845 (m-40) REVERT: A 74 PHE cc_start: 0.8140 (t80) cc_final: 0.7867 (t80) REVERT: A 93 TRP cc_start: 0.7267 (t-100) cc_final: 0.6971 (t-100) REVERT: A 216 ARG cc_start: 0.7773 (ptp-110) cc_final: 0.7536 (ptp-110) REVERT: A 222 ARG cc_start: 0.8024 (mpt-90) cc_final: 0.7425 (ptt180) REVERT: A 234 MET cc_start: 0.8007 (mmm) cc_final: 0.7381 (mtt) REVERT: A 273 ASP cc_start: 0.8538 (t0) cc_final: 0.8079 (t0) REVERT: A 277 PHE cc_start: 0.7993 (m-80) cc_final: 0.7389 (m-80) outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 0.5070 time to fit residues: 86.8071 Evaluate side-chains 156 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.082229 restraints weight = 11503.360| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.84 r_work: 0.2796 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8922 Z= 0.131 Angle : 0.553 9.452 12099 Z= 0.292 Chirality : 0.043 0.201 1372 Planarity : 0.004 0.058 1526 Dihedral : 4.425 31.252 1218 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 19.11 % Favored : 78.40 % 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: 0.55 (0.26), residues: 1109 helix: 2.28 (0.28), residues: 358 sheet: -0.27 (0.29), residues: 277 loop : -0.71 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 160 TYR 0.033 0.001 TYR S 235 PHE 0.010 0.001 PHE A 197 TRP 0.022 0.001 TRP A 188 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8917) covalent geometry : angle 0.55244 / 0.29 (12089) SS BOND : bond 0.00361 / 0.19 ( 5) SS BOND : angle 0.69505 / 0.38 ( 10) hydrogen bonds : bond 0.03401 / 2.26 ( 450) hydrogen bonds : angle 4.49708 / 3.26 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.236 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: C 20 ASP cc_start: 0.8326 (m-30) cc_final: 0.8067 (m-30) REVERT: C 21 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6238 (ttp80) REVERT: C 276 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8645 (mm-30) REVERT: C 305 CYS cc_start: 0.8180 (m) cc_final: 0.7794 (m) REVERT: C 349 LYS cc_start: 0.8041 (ttpp) cc_final: 0.7796 (ttmm) REVERT: B 13 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: B 23 LYS cc_start: 0.8320 (mmmm) cc_final: 0.8117 (ttmm) REVERT: B 217 MET cc_start: 0.8161 (ptt) cc_final: 0.7788 (pmm) REVERT: B 258 ASP cc_start: 0.8313 (t70) cc_final: 0.7697 (t0) REVERT: G 48 ASP cc_start: 0.8824 (t0) cc_final: 0.8550 (t0) REVERT: S 186 GLN cc_start: 0.8253 (tt0) cc_final: 0.7963 (pt0) REVERT: S 235 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6179 (t80) REVERT: A 45 ASN cc_start: 0.8294 (m-40) cc_final: 0.7841 (m-40) REVERT: A 68 ASN cc_start: 0.8093 (m110) cc_final: 0.7822 (m-40) REVERT: A 74 PHE cc_start: 0.8152 (t80) cc_final: 0.7871 (t80) REVERT: A 93 TRP cc_start: 0.7221 (t-100) cc_final: 0.6934 (t-100) REVERT: A 222 ARG cc_start: 0.8053 (mpt-90) cc_final: 0.7426 (ptt180) REVERT: A 277 PHE cc_start: 0.7992 (m-80) cc_final: 0.7400 (m-80) outliers start: 23 outliers final: 14 residues processed: 155 average time/residue: 0.5504 time to fit residues: 90.5597 Evaluate side-chains 157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 64 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 GLN C 204 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.080514 restraints weight = 11650.537| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.87 r_work: 0.2804 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8922 Z= 0.183 Angle : 0.591 12.416 12099 Z= 0.310 Chirality : 0.045 0.208 1372 Planarity : 0.004 0.058 1526 Dihedral : 4.434 33.545 1216 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.76 % Rotamer: Outliers : 2.70 % Allowed : 19.11 % Favored : 78.19 % 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: 0.51 (0.26), residues: 1109 helix: 2.21 (0.28), residues: 358 sheet: -0.25 (0.29), residues: 287 loop : -0.72 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 160 TYR 0.035 0.002 TYR S 235 PHE 0.012 0.001 PHE A 197 TRP 0.031 0.001 TRP A 188 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 8917) covalent geometry : angle 0.59041 / 0.31 (12089) SS BOND : bond 0.00411 / 0.21 ( 5) SS BOND : angle 0.80091 / 0.44 ( 10) hydrogen bonds : bond 0.03664 / 2.43 ( 450) hydrogen bonds : angle 4.61665 / 3.33 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.268 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: C 21 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6309 (ttp80) REVERT: C 205 ARG cc_start: 0.8448 (mmp80) cc_final: 0.8232 (mmp80) REVERT: C 276 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8618 (mm-30) REVERT: C 305 CYS cc_start: 0.8237 (m) cc_final: 0.7823 (m) REVERT: C 349 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7844 (ttmm) REVERT: B 13 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8059 (pp30) REVERT: B 101 MET cc_start: 0.8805 (ptm) cc_final: 0.8544 (ptm) REVERT: B 217 MET cc_start: 0.8161 (ptt) cc_final: 0.7770 (pmm) REVERT: B 260 GLU cc_start: 0.8920 (tt0) cc_final: 0.8664 (tt0) REVERT: G 48 ASP cc_start: 0.8898 (t0) cc_final: 0.8639 (t0) REVERT: S 82 GLN cc_start: 0.8668 (tp40) cc_final: 0.8450 (mm-40) REVERT: S 186 GLN cc_start: 0.8296 (tt0) cc_final: 0.8046 (pt0) REVERT: S 235 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6288 (t80) REVERT: A 45 ASN cc_start: 0.8352 (m-40) cc_final: 0.7902 (m-40) REVERT: A 93 TRP cc_start: 0.7244 (t-100) cc_final: 0.6997 (t-100) REVERT: A 222 ARG cc_start: 0.8063 (mpt-90) cc_final: 0.7487 (ptt180) REVERT: A 234 MET cc_start: 0.8148 (mmm) cc_final: 0.7448 (mtt) REVERT: A 277 PHE cc_start: 0.8034 (m-80) cc_final: 0.7455 (m-80) outliers start: 25 outliers final: 15 residues processed: 158 average time/residue: 0.5693 time to fit residues: 95.3474 Evaluate side-chains 160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 237 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.131645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.082168 restraints weight = 11558.128| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.85 r_work: 0.2789 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8922 Z= 0.135 Angle : 0.573 11.581 12099 Z= 0.301 Chirality : 0.044 0.246 1372 Planarity : 0.004 0.058 1526 Dihedral : 4.362 31.650 1216 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 2.05 % Allowed : 20.30 % Favored : 77.65 % 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: 0.52 (0.26), residues: 1109 helix: 2.26 (0.28), residues: 358 sheet: -0.28 (0.29), residues: 277 loop : -0.73 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 160 TYR 0.033 0.001 TYR S 235 PHE 0.013 0.001 PHE A 74 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8917) covalent geometry : angle 0.57328 / 0.30 (12089) SS BOND : bond 0.00351 / 0.18 ( 5) SS BOND : angle 0.75194 / 0.41 ( 10) hydrogen bonds : bond 0.03560 / 2.38 ( 450) hydrogen bonds : angle 4.60129 / 3.32 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.274 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: C 9 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: C 21 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6249 (ttp80) REVERT: C 205 ARG cc_start: 0.8434 (mmp80) cc_final: 0.8002 (mmp80) REVERT: C 276 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8610 (mm-30) REVERT: C 305 CYS cc_start: 0.8186 (m) cc_final: 0.7790 (m) REVERT: C 349 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7794 (ttmm) REVERT: B 13 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8043 (pp30) REVERT: B 23 LYS cc_start: 0.8325 (mtpp) cc_final: 0.8078 (ttmm) REVERT: B 101 MET cc_start: 0.8765 (ptm) cc_final: 0.8500 (ptm) REVERT: B 217 MET cc_start: 0.8139 (ptt) cc_final: 0.7767 (pmm) REVERT: B 258 ASP cc_start: 0.8307 (t70) cc_final: 0.7689 (t0) REVERT: B 260 GLU cc_start: 0.8855 (tt0) cc_final: 0.8625 (tt0) REVERT: G 48 ASP cc_start: 0.8829 (t0) cc_final: 0.8547 (t0) REVERT: S 186 GLN cc_start: 0.8242 (tt0) cc_final: 0.7949 (pt0) REVERT: S 235 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6082 (t80) REVERT: A 45 ASN cc_start: 0.8302 (m-40) cc_final: 0.7852 (m-40) REVERT: A 68 ASN cc_start: 0.8018 (m110) cc_final: 0.7766 (m-40) REVERT: A 216 ARG cc_start: 0.7752 (ptp-110) cc_final: 0.7504 (ptp-110) REVERT: A 222 ARG cc_start: 0.8069 (mpt-90) cc_final: 0.7451 (ptt180) REVERT: A 234 MET cc_start: 0.8113 (mmm) cc_final: 0.7379 (mtt) REVERT: A 277 PHE cc_start: 0.8023 (m-80) cc_final: 0.7483 (m-80) outliers start: 19 outliers final: 12 residues processed: 156 average time/residue: 0.5419 time to fit residues: 89.6510 Evaluate side-chains 160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 chunk 94 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 237 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082361 restraints weight = 11562.841| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.86 r_work: 0.2818 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8922 Z= 0.131 Angle : 0.571 11.408 12099 Z= 0.301 Chirality : 0.044 0.256 1372 Planarity : 0.004 0.058 1526 Dihedral : 4.341 30.697 1216 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.05 % Allowed : 20.30 % Favored : 77.65 % 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: 0.54 (0.26), residues: 1109 helix: 2.26 (0.28), residues: 358 sheet: -0.31 (0.29), residues: 284 loop : -0.68 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG S 160 TYR 0.032 0.001 TYR S 235 PHE 0.026 0.001 PHE A 74 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8917) covalent geometry : angle 0.57056 / 0.30 (12089) SS BOND : bond 0.00339 / 0.17 ( 5) SS BOND : angle 0.78799 / 0.43 ( 10) hydrogen bonds : bond 0.03539 / 2.37 ( 450) hydrogen bonds : angle 4.59097 / 3.31 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3452.46 seconds wall clock time: 59 minutes 27.64 seconds (3567.64 seconds total)