Starting phenix.real_space_refine on Tue Mar 3 13:38:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x4s_22042/03_2026/6x4s_22042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x4s_22042/03_2026/6x4s_22042.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/6x4s_22042/03_2026/6x4s_22042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x4s_22042/03_2026/6x4s_22042.map" model { file = "/net/cci-nas-00/data/ceres_data/6x4s_22042/03_2026/6x4s_22042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x4s_22042/03_2026/6x4s_22042.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= 0.000 sd= 0.002 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 Ca 1 9.91 5 S 15 5.16 5 C 3521 2.51 5 N 890 2.21 5 O 946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5373 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1158 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "B" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1170 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 4, 'GLU:plan': 8, 'HIS:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1155 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1165 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 4, 'GLU:plan': 8, 'HIS:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 81 Chain: "E" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.41, per 1000 atoms: 0.26 Number of scatterers: 5373 At special positions: 0 Unit cell: (68.544, 69.632, 120.768, 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) Ca 1 19.99 S 15 16.00 O 946 8.00 N 890 7.00 C 3521 6.00 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: 0.46 Conformation dependent library (CDL) restraints added in 420.6 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 91.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.776A pdb=" N LEU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 254 removed outlier: 3.773A pdb=" N GLN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.946A pdb=" N ARG A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.604A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 313 through 336 Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 194 through 256 removed outlier: 3.521A pdb=" N LYS B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 4.295A pdb=" N ARG B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 300 Processing helix chain 'B' and resid 313 through 336 Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 194 through 256 removed outlier: 3.683A pdb=" N GLN C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.706A pdb=" N ARG C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 4.545A pdb=" N VAL C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 308 Processing helix chain 'C' and resid 313 through 336 Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 197 through 256 Proline residue: D 216 - end of helix removed outlier: 3.987A pdb=" N ARG D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 300 removed outlier: 3.872A pdb=" N THR D 267 " --> pdb=" O MET D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 336 removed outlier: 3.522A pdb=" N TYR D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 Proline residue: E 76 - end of helix Processing helix chain 'F' and resid 69 through 92 Proline residue: F 76 - end of helix Processing helix chain 'G' and resid 69 through 92 Proline residue: G 76 - end of helix Processing helix chain 'H' and resid 69 through 92 Proline residue: H 76 - end of helix 519 hydrogen bonds defined for protein. 1557 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: 0.90 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1689 1.34 - 1.46: 894 1.46 - 1.57: 2851 1.57 - 1.69: 2 1.69 - 1.81: 30 Bond restraints: 5466 Sorted by residual: bond pdb=" CA VAL A 294 " pdb=" C VAL A 294 " ideal model delta sigma weight residual 1.525 1.468 0.057 2.10e-02 2.27e+03 7.33e+00 bond pdb=" N LYS C 308 " pdb=" CA LYS C 308 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.46e-02 4.69e+03 5.75e+00 bond pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.52e-02 4.33e+03 5.75e+00 bond pdb=" CB VAL A 294 " pdb=" CG1 VAL A 294 " ideal model delta sigma weight residual 1.521 1.593 -0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" CG GLU B 257 " pdb=" CD GLU B 257 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.78e+00 ... (remaining 5461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 7161 1.68 - 3.37: 237 3.37 - 5.05: 42 5.05 - 6.73: 16 6.73 - 8.42: 4 Bond angle restraints: 7460 Sorted by residual: angle pdb=" CD1 LEU D 291 " pdb=" CG LEU D 291 " pdb=" CD2 LEU D 291 " ideal model delta sigma weight residual 110.80 103.62 7.18 2.20e+00 2.07e-01 1.07e+01 angle pdb=" C ASP D 330 " pdb=" CA ASP D 330 " pdb=" CB ASP D 330 " ideal model delta sigma weight residual 110.85 116.27 -5.42 1.70e+00 3.46e-01 1.02e+01 angle pdb=" C MET A 263 " pdb=" N GLU A 264 " pdb=" CA GLU A 264 " ideal model delta sigma weight residual 121.80 115.69 6.11 2.44e+00 1.68e-01 6.28e+00 angle pdb=" CA LEU C 253 " pdb=" CB LEU C 253 " pdb=" CG LEU C 253 " ideal model delta sigma weight residual 116.30 124.72 -8.42 3.50e+00 8.16e-02 5.78e+00 angle pdb=" CA ARG D 252 " pdb=" CB ARG D 252 " pdb=" CG ARG D 252 " ideal model delta sigma weight residual 114.10 109.37 4.73 2.00e+00 2.50e-01 5.60e+00 ... (remaining 7455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 2759 15.84 - 31.69: 323 31.69 - 47.53: 104 47.53 - 63.38: 17 63.38 - 79.22: 5 Dihedral angle restraints: 3208 sinusoidal: 1128 harmonic: 2080 Sorted by residual: dihedral pdb=" CA ALA A 307 " pdb=" C ALA A 307 " pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ARG A 193 " pdb=" C ARG A 193 " pdb=" N GLU A 194 " pdb=" CA GLU A 194 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ALA C 307 " pdb=" C ALA C 307 " pdb=" N LYS C 308 " pdb=" CA LYS C 308 " ideal model delta harmonic sigma weight residual 180.00 164.50 15.50 0 5.00e+00 4.00e-02 9.61e+00 ... (remaining 3205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 895 0.115 - 0.229: 22 0.229 - 0.344: 2 0.344 - 0.459: 0 0.459 - 0.574: 1 Chirality restraints: 920 Sorted by residual: chirality pdb=" CG LEU D 291 " pdb=" CB LEU D 291 " pdb=" CD1 LEU D 291 " pdb=" CD2 LEU D 291 " both_signs ideal model delta sigma weight residual False -2.59 -3.16 0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" CB VAL A 294 " pdb=" CA VAL A 294 " pdb=" CG1 VAL A 294 " pdb=" CG2 VAL A 294 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU D 291 " pdb=" N LEU D 291 " pdb=" C LEU D 291 " pdb=" CB LEU D 291 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 917 not shown) Planarity restraints: 910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 330 " -0.024 2.00e-02 2.50e+03 4.82e-02 2.33e+01 pdb=" CG ASP D 330 " 0.083 2.00e-02 2.50e+03 pdb=" OD1 ASP D 330 " -0.031 2.00e-02 2.50e+03 pdb=" OD2 ASP D 330 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 307 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ALA A 307 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 307 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 308 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 307 " 0.014 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ALA C 307 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA C 307 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 308 " 0.016 2.00e-02 2.50e+03 ... (remaining 907 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 39 2.64 - 3.21: 5207 3.21 - 3.77: 8739 3.77 - 4.34: 10111 4.34 - 4.90: 16782 Nonbonded interactions: 40878 Sorted by model distance: nonbonded pdb=" OE2 GLU D 264 " pdb="CA CA A 501 " model vdw 2.077 2.510 nonbonded pdb=" OE2 GLU C 264 " pdb="CA CA A 501 " model vdw 2.213 2.510 nonbonded pdb=" O ASP B 178 " pdb=" OG1 THR B 181 " model vdw 2.219 3.040 nonbonded pdb=" O VAL B 201 " pdb=" OG1 THR B 204 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLN D 246 " pdb=" OG1 THR D 274 " model vdw 2.289 3.040 ... (remaining 40873 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 178 through 191 or (resid 192 through 196 and (name N or n \ ame CA or name C or name O or name CB )) or resid 197 through 199 or (resid 200 \ and (name N or name CA or name C or name O or name CB )) or resid 201 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 221 through 241 or (resid 242 through 243 and (name N or \ name CA or name C or name O or name CB )) or resid 244 through 286 or resid 302 \ or resid 312 through 327 or (resid 328 and (name N or name CA or name C or name \ O or name CB )) or resid 329 through 336)) selection = (chain 'B' and (resid 178 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 183 or (resid 184 through 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 18 \ 7 or (resid 188 through 189 and (name N or name CA or name C or name O or name C \ B )) or resid 190 or (resid 191 through 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 or (resid 198 through 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 224 or (resid 225 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 241 or \ (resid 242 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 286 or (resid 291 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 336)) selection = (chain 'C' and (resid 178 through 191 or (resid 192 through 196 and (name N or n \ ame CA or name C or name O or name CB )) or resid 197 through 199 or (resid 200 \ and (name N or name CA or name C or name O or name CB )) or resid 201 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 221 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 286 or resid 302 or resid 31 \ 2 through 327 or (resid 328 and (name N or name CA or name C or name O or name C \ B )) or resid 329 through 336)) selection = (chain 'D' and (resid 178 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 183 or (resid 184 through 185 \ and (name N or name CA or name C or name O or name CB )) or resid 186 through 18 \ 7 or (resid 188 through 189 and (name N or name CA or name C or name O or name C \ B )) or resid 190 or (resid 191 through 196 and (name N or name CA or name C or \ name O or name CB )) or resid 197 or (resid 198 through 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 224 or (resid 225 and \ (name N or name CA or name C or name O or name CB )) or resid 226 through 241 or \ (resid 242 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 286 or (resid 291 and (name N or name CA or name C or name \ O or name CB )) or resid 312 through 336)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.360 Find NCS groups from input model: 0.120 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.007 0.072 5466 Z= 0.295 Angle : 0.768 8.418 7460 Z= 0.404 Chirality : 0.050 0.574 920 Planarity : 0.004 0.048 910 Dihedral : 15.586 79.222 1852 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.97 % Allowed : 21.94 % Favored : 77.09 % 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: 1.34 (0.30), residues: 682 helix: 1.29 (0.19), residues: 636 sheet: None (None), residues: 0 loop : -4.42 (0.58), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 231 TYR 0.013 0.002 TYR C 258 PHE 0.011 0.002 PHE D 247 TRP 0.025 0.002 TRP B 260 HIS 0.006 0.002 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 5466) covalent geometry : angle 0.76784 ( 7460) hydrogen bonds : bond 0.10803 ( 519) hydrogen bonds : angle 4.68424 ( 1557) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.7739 (tmm-80) cc_final: 0.7380 (tmm-80) REVERT: A 317 TYR cc_start: 0.9238 (t80) cc_final: 0.8677 (t80) REVERT: A 321 LYS cc_start: 0.8763 (mttt) cc_final: 0.8372 (ttmm) REVERT: A 328 GLU cc_start: 0.8547 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 211 GLN cc_start: 0.8862 (mt0) cc_final: 0.8533 (mm-40) REVERT: B 230 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.7338 (ptm160) REVERT: B 243 MET cc_start: 0.7462 (mtp) cc_final: 0.7033 (mtt) REVERT: B 253 LEU cc_start: 0.8766 (mt) cc_final: 0.8526 (mp) REVERT: B 263 MET cc_start: 0.8190 (mmm) cc_final: 0.7861 (ttm) REVERT: B 313 ASP cc_start: 0.8041 (t0) cc_final: 0.7811 (t0) REVERT: B 316 GLN cc_start: 0.7632 (pt0) cc_final: 0.7311 (tt0) REVERT: B 318 ASN cc_start: 0.8886 (t0) cc_final: 0.8636 (m-40) REVERT: C 226 GLN cc_start: 0.8819 (tt0) cc_final: 0.8271 (tt0) REVERT: C 229 ASN cc_start: 0.8826 (m-40) cc_final: 0.8594 (t0) REVERT: C 235 MET cc_start: 0.8076 (tpp) cc_final: 0.7622 (tmm) REVERT: C 246 GLN cc_start: 0.9072 (tt0) cc_final: 0.8859 (tt0) REVERT: C 247 PHE cc_start: 0.9312 (t80) cc_final: 0.8944 (t80) REVERT: C 263 MET cc_start: 0.8537 (mmm) cc_final: 0.8172 (tpp) REVERT: C 276 MET cc_start: 0.7603 (mtp) cc_final: 0.7226 (mmp) REVERT: C 317 TYR cc_start: 0.9096 (t80) cc_final: 0.8694 (t80) REVERT: C 328 GLU cc_start: 0.8459 (tt0) cc_final: 0.7984 (pt0) REVERT: D 256 TRP cc_start: 0.8287 (m-90) cc_final: 0.7796 (m-90) REVERT: D 260 TRP cc_start: 0.8026 (t-100) cc_final: 0.7806 (t-100) REVERT: D 262 ILE cc_start: 0.8261 (tt) cc_final: 0.8001 (tt) REVERT: E 90 ASN cc_start: 0.6849 (m-40) cc_final: 0.6369 (m110) REVERT: F 70 LEU cc_start: 0.9020 (tt) cc_final: 0.8567 (mp) REVERT: F 73 THR cc_start: 0.8314 (p) cc_final: 0.8105 (p) REVERT: H 70 LEU cc_start: 0.8870 (tt) cc_final: 0.8512 (mp) outliers start: 5 outliers final: 0 residues processed: 266 average time/residue: 0.0913 time to fit residues: 29.6076 Evaluate side-chains 206 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 315 ASN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.126790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103753 restraints weight = 13359.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107192 restraints weight = 6862.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.109545 restraints weight = 4703.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110593 restraints weight = 3733.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.111768 restraints weight = 3291.917| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5466 Z= 0.169 Angle : 0.672 8.008 7460 Z= 0.340 Chirality : 0.037 0.183 920 Planarity : 0.004 0.029 910 Dihedral : 3.642 17.402 748 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.27 % Allowed : 28.35 % Favored : 67.38 % 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: 3.84 (0.32), residues: 682 helix: 2.96 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -2.97 (0.65), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 252 TYR 0.014 0.002 TYR C 187 PHE 0.011 0.001 PHE C 247 TRP 0.016 0.001 TRP B 260 HIS 0.004 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 5466) covalent geometry : angle 0.67193 ( 7460) hydrogen bonds : bond 0.04906 ( 519) hydrogen bonds : angle 3.29155 ( 1557) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8702 (mtmt) REVERT: A 272 TYR cc_start: 0.8594 (t80) cc_final: 0.8266 (t80) REVERT: B 243 MET cc_start: 0.7215 (mtp) cc_final: 0.6978 (mmt) REVERT: B 246 GLN cc_start: 0.9011 (tt0) cc_final: 0.8802 (tt0) REVERT: B 316 GLN cc_start: 0.7704 (pt0) cc_final: 0.7477 (tt0) REVERT: C 221 LYS cc_start: 0.9137 (ttmt) cc_final: 0.8924 (ttpt) REVERT: C 235 MET cc_start: 0.7976 (tpp) cc_final: 0.7749 (tmm) REVERT: C 247 PHE cc_start: 0.9318 (t80) cc_final: 0.9068 (t80) REVERT: D 213 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8529 (tm-30) REVERT: D 226 GLN cc_start: 0.8566 (pp30) cc_final: 0.8365 (pp30) REVERT: F 70 LEU cc_start: 0.8880 (tt) cc_final: 0.8365 (mp) REVERT: H 70 LEU cc_start: 0.8862 (tt) cc_final: 0.8442 (mp) outliers start: 22 outliers final: 16 residues processed: 234 average time/residue: 0.0876 time to fit residues: 25.4310 Evaluate side-chains 222 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 GLN B 246 GLN C 226 GLN C 229 ASN C 315 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.101578 restraints weight = 13121.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.105062 restraints weight = 6669.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107251 restraints weight = 4542.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108420 restraints weight = 3626.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109390 restraints weight = 3193.504| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5466 Z= 0.157 Angle : 0.613 7.987 7460 Z= 0.311 Chirality : 0.036 0.138 920 Planarity : 0.004 0.028 910 Dihedral : 3.521 15.602 748 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.44 % Allowed : 28.93 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.16 (0.32), residues: 682 helix: 3.05 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.62 (0.81), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 231 TYR 0.016 0.002 TYR A 317 PHE 0.023 0.001 PHE B 247 TRP 0.013 0.001 TRP A 260 HIS 0.004 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5466) covalent geometry : angle 0.61327 ( 7460) hydrogen bonds : bond 0.04595 ( 519) hydrogen bonds : angle 3.17866 ( 1557) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8701 (ttmt) REVERT: A 226 GLN cc_start: 0.8716 (tt0) cc_final: 0.8347 (tt0) REVERT: A 272 TYR cc_start: 0.8598 (t80) cc_final: 0.8277 (t80) REVERT: B 226 GLN cc_start: 0.8256 (pp30) cc_final: 0.7863 (pp30) REVERT: B 243 MET cc_start: 0.7323 (mtp) cc_final: 0.7046 (mmt) REVERT: B 316 GLN cc_start: 0.7835 (pt0) cc_final: 0.7542 (tt0) REVERT: C 221 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8784 (ttmt) REVERT: C 226 GLN cc_start: 0.8842 (tt0) cc_final: 0.8636 (tt0) REVERT: C 235 MET cc_start: 0.8066 (tpp) cc_final: 0.7721 (tmm) REVERT: C 246 GLN cc_start: 0.9151 (tt0) cc_final: 0.8939 (tt0) REVERT: D 213 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 226 GLN cc_start: 0.8617 (pp30) cc_final: 0.8392 (pp30) REVERT: D 326 LYS cc_start: 0.8960 (tppt) cc_final: 0.8760 (tppt) REVERT: D 329 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8693 (tt) REVERT: F 70 LEU cc_start: 0.8964 (tt) cc_final: 0.8479 (mp) REVERT: H 70 LEU cc_start: 0.8884 (tt) cc_final: 0.8582 (mp) outliers start: 28 outliers final: 16 residues processed: 223 average time/residue: 0.0875 time to fit residues: 24.2245 Evaluate side-chains 220 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 56 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 overall best weight: 0.1936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.128699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.105688 restraints weight = 12183.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109077 restraints weight = 6367.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111256 restraints weight = 4352.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.112539 restraints weight = 3446.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.113492 restraints weight = 3018.886| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5466 Z= 0.130 Angle : 0.595 7.859 7460 Z= 0.295 Chirality : 0.034 0.133 920 Planarity : 0.003 0.027 910 Dihedral : 3.509 15.611 748 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.88 % Allowed : 32.82 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.33 (0.32), residues: 682 helix: 3.17 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.60 (0.80), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.017 0.002 TYR A 317 PHE 0.019 0.001 PHE B 247 TRP 0.010 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5466) covalent geometry : angle 0.59518 ( 7460) hydrogen bonds : bond 0.04176 ( 519) hydrogen bonds : angle 2.95302 ( 1557) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8246 (pp30) cc_final: 0.7792 (pp30) REVERT: B 234 TRP cc_start: 0.8091 (t60) cc_final: 0.7725 (t60) REVERT: B 243 MET cc_start: 0.7250 (mtp) cc_final: 0.7008 (mmt) REVERT: B 316 GLN cc_start: 0.7808 (pt0) cc_final: 0.7568 (tt0) REVERT: B 317 TYR cc_start: 0.9145 (t80) cc_final: 0.8908 (t80) REVERT: B 321 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8873 (mmtp) REVERT: C 226 GLN cc_start: 0.8815 (tt0) cc_final: 0.8601 (tt0) REVERT: C 235 MET cc_start: 0.7858 (tpp) cc_final: 0.7604 (tmm) REVERT: C 246 GLN cc_start: 0.9038 (tt0) cc_final: 0.8821 (tt0) REVERT: C 272 TYR cc_start: 0.8453 (t80) cc_final: 0.8109 (t80) REVERT: D 226 GLN cc_start: 0.8585 (pp30) cc_final: 0.8371 (pp30) REVERT: D 246 GLN cc_start: 0.8827 (tt0) cc_final: 0.8466 (tt0) REVERT: D 326 LYS cc_start: 0.8979 (tppt) cc_final: 0.8758 (tppt) REVERT: D 329 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8627 (tt) REVERT: F 70 LEU cc_start: 0.8986 (tt) cc_final: 0.8419 (mp) REVERT: H 70 LEU cc_start: 0.8919 (tt) cc_final: 0.8547 (mp) outliers start: 20 outliers final: 15 residues processed: 220 average time/residue: 0.0833 time to fit residues: 22.6386 Evaluate side-chains 213 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.0020 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN E 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.126817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103040 restraints weight = 13325.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106582 restraints weight = 7072.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108791 restraints weight = 4931.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109715 restraints weight = 3967.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.111070 restraints weight = 3546.444| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5466 Z= 0.150 Angle : 0.616 7.774 7460 Z= 0.309 Chirality : 0.035 0.179 920 Planarity : 0.003 0.023 910 Dihedral : 3.399 15.674 748 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.83 % Allowed : 33.01 % Favored : 61.17 % 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: 4.29 (0.32), residues: 682 helix: 3.13 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.73 (0.84), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 286 TYR 0.020 0.002 TYR A 317 PHE 0.028 0.001 PHE C 247 TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5466) covalent geometry : angle 0.61636 ( 7460) hydrogen bonds : bond 0.04217 ( 519) hydrogen bonds : angle 3.07369 ( 1557) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8336 (pp30) cc_final: 0.7834 (pp30) REVERT: B 234 TRP cc_start: 0.8138 (t60) cc_final: 0.7836 (t60) REVERT: B 243 MET cc_start: 0.7467 (mtp) cc_final: 0.7029 (mmt) REVERT: B 263 MET cc_start: 0.7942 (ttm) cc_final: 0.7659 (ttm) REVERT: B 316 GLN cc_start: 0.7876 (pt0) cc_final: 0.7667 (tt0) REVERT: C 220 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8744 (ttmt) REVERT: C 226 GLN cc_start: 0.8860 (tt0) cc_final: 0.8630 (tt0) REVERT: C 235 MET cc_start: 0.8054 (tpp) cc_final: 0.7623 (tmm) REVERT: D 231 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7837 (tmm-80) REVERT: D 326 LYS cc_start: 0.9062 (tppt) cc_final: 0.8817 (tppt) REVERT: D 329 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8720 (tt) REVERT: F 70 LEU cc_start: 0.9050 (tt) cc_final: 0.8550 (mp) REVERT: H 70 LEU cc_start: 0.8950 (tt) cc_final: 0.8609 (mp) outliers start: 30 outliers final: 19 residues processed: 221 average time/residue: 0.0853 time to fit residues: 23.3898 Evaluate side-chains 218 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 304 HIS ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 315 ASN C 323 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.126379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.103252 restraints weight = 13089.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.106603 restraints weight = 7013.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108793 restraints weight = 4899.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109762 restraints weight = 3951.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.110881 restraints weight = 3520.876| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5466 Z= 0.139 Angle : 0.618 10.909 7460 Z= 0.306 Chirality : 0.035 0.168 920 Planarity : 0.003 0.026 910 Dihedral : 3.372 16.074 748 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.83 % Allowed : 32.04 % Favored : 62.14 % 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: 4.30 (0.32), residues: 682 helix: 3.19 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.94 (0.79), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.024 0.002 TYR A 258 PHE 0.023 0.001 PHE C 247 TRP 0.009 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5466) covalent geometry : angle 0.61826 ( 7460) hydrogen bonds : bond 0.04113 ( 519) hydrogen bonds : angle 3.06333 ( 1557) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.7763 (ttm) cc_final: 0.7392 (ttm) REVERT: B 226 GLN cc_start: 0.8357 (pp30) cc_final: 0.7840 (pp30) REVERT: B 234 TRP cc_start: 0.8109 (t60) cc_final: 0.7804 (t60) REVERT: B 243 MET cc_start: 0.7420 (mtp) cc_final: 0.7027 (mmt) REVERT: B 316 GLN cc_start: 0.7857 (pt0) cc_final: 0.7606 (tt0) REVERT: C 219 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7794 (mt-10) REVERT: C 221 LYS cc_start: 0.9139 (tttt) cc_final: 0.8875 (ttmt) REVERT: C 226 GLN cc_start: 0.8841 (tt0) cc_final: 0.8613 (tt0) REVERT: C 235 MET cc_start: 0.7991 (tpp) cc_final: 0.7567 (tmm) REVERT: C 246 GLN cc_start: 0.9211 (tt0) cc_final: 0.8890 (tt0) REVERT: D 231 ARG cc_start: 0.8066 (ttt90) cc_final: 0.7810 (tmm-80) REVERT: D 329 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8760 (tt) REVERT: F 70 LEU cc_start: 0.9032 (tt) cc_final: 0.8553 (mp) REVERT: G 90 ASN cc_start: 0.6962 (m110) cc_final: 0.6758 (m-40) REVERT: H 70 LEU cc_start: 0.8892 (tt) cc_final: 0.8529 (mp) outliers start: 30 outliers final: 23 residues processed: 213 average time/residue: 0.0818 time to fit residues: 21.6950 Evaluate side-chains 216 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain H residue 69 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.125401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.102210 restraints weight = 12992.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105644 restraints weight = 6807.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107848 restraints weight = 4675.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.109349 restraints weight = 3734.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.109716 restraints weight = 3219.036| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5466 Z= 0.171 Angle : 0.661 9.008 7460 Z= 0.331 Chirality : 0.036 0.147 920 Planarity : 0.003 0.026 910 Dihedral : 3.401 15.884 748 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 6.02 % Allowed : 33.01 % Favored : 60.97 % 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: 4.12 (0.32), residues: 682 helix: 3.07 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -3.09 (0.78), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.018 0.002 TYR A 317 PHE 0.022 0.001 PHE C 247 TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5466) covalent geometry : angle 0.66080 ( 7460) hydrogen bonds : bond 0.04316 ( 519) hydrogen bonds : angle 3.27888 ( 1557) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.7893 (ttm) cc_final: 0.7317 (ttm) REVERT: B 226 GLN cc_start: 0.8398 (pp30) cc_final: 0.7876 (pp30) REVERT: B 234 TRP cc_start: 0.8164 (t60) cc_final: 0.7843 (t60) REVERT: B 243 MET cc_start: 0.7303 (mtp) cc_final: 0.7074 (mmt) REVERT: B 316 GLN cc_start: 0.7978 (pt0) cc_final: 0.7684 (tt0) REVERT: B 321 LYS cc_start: 0.9113 (mmtp) cc_final: 0.8884 (mmtm) REVERT: C 219 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7864 (mt-10) REVERT: C 235 MET cc_start: 0.8021 (tpp) cc_final: 0.7633 (tmm) REVERT: D 231 ARG cc_start: 0.8129 (ttt90) cc_final: 0.7865 (tmm-80) REVERT: D 329 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8793 (tt) REVERT: F 70 LEU cc_start: 0.9036 (tt) cc_final: 0.8554 (mp) REVERT: H 70 LEU cc_start: 0.8887 (tt) cc_final: 0.8565 (mp) outliers start: 31 outliers final: 27 residues processed: 205 average time/residue: 0.0851 time to fit residues: 21.7228 Evaluate side-chains 216 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain H residue 69 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 0.0000 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 226 GLN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099459 restraints weight = 12484.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.102826 restraints weight = 6250.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.105157 restraints weight = 4201.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.106627 restraints weight = 3306.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107506 restraints weight = 2849.742| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5466 Z= 0.150 Angle : 0.653 9.039 7460 Z= 0.326 Chirality : 0.037 0.190 920 Planarity : 0.003 0.030 910 Dihedral : 3.465 15.774 748 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.24 % Allowed : 32.82 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.09 (0.32), residues: 682 helix: 3.01 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.93 (0.82), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 230 TYR 0.019 0.002 TYR C 317 PHE 0.024 0.001 PHE B 247 TRP 0.010 0.001 TRP C 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5466) covalent geometry : angle 0.65299 ( 7460) hydrogen bonds : bond 0.04236 ( 519) hydrogen bonds : angle 3.24342 ( 1557) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.7582 (ttm) cc_final: 0.7061 (ttm) REVERT: B 226 GLN cc_start: 0.8350 (pp30) cc_final: 0.7821 (pp30) REVERT: B 243 MET cc_start: 0.7598 (mtp) cc_final: 0.7134 (mmt) REVERT: B 316 GLN cc_start: 0.7992 (pt0) cc_final: 0.7666 (tt0) REVERT: C 219 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7905 (mt-10) REVERT: C 235 MET cc_start: 0.8018 (tpp) cc_final: 0.7450 (tmm) REVERT: D 213 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 329 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8604 (tt) REVERT: F 70 LEU cc_start: 0.9048 (tt) cc_final: 0.8573 (mp) REVERT: H 70 LEU cc_start: 0.8975 (tt) cc_final: 0.8574 (mp) outliers start: 27 outliers final: 25 residues processed: 205 average time/residue: 0.0800 time to fit residues: 20.5555 Evaluate side-chains 217 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 69 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** 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 = 0.4009 r_free = 0.4009 target = 0.127018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104584 restraints weight = 12423.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.107902 restraints weight = 6510.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110075 restraints weight = 4456.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.111263 restraints weight = 3523.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.112255 restraints weight = 3085.775| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5466 Z= 0.138 Angle : 0.655 8.268 7460 Z= 0.325 Chirality : 0.036 0.184 920 Planarity : 0.003 0.024 910 Dihedral : 3.510 15.856 748 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.05 % Allowed : 33.98 % Favored : 60.97 % 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: 4.13 (0.32), residues: 682 helix: 3.09 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.72 (0.74), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 286 TYR 0.015 0.002 TYR A 317 PHE 0.022 0.001 PHE B 247 TRP 0.015 0.001 TRP B 234 HIS 0.000 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5466) covalent geometry : angle 0.65543 ( 7460) hydrogen bonds : bond 0.04107 ( 519) hydrogen bonds : angle 3.21971 ( 1557) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.7601 (ttm) cc_final: 0.7212 (ttm) REVERT: B 226 GLN cc_start: 0.8372 (pp30) cc_final: 0.7936 (pp30) REVERT: B 234 TRP cc_start: 0.8008 (t60) cc_final: 0.7688 (t60) REVERT: B 257 GLU cc_start: 0.7455 (mp0) cc_final: 0.7227 (mp0) REVERT: B 316 GLN cc_start: 0.7876 (pt0) cc_final: 0.7590 (tt0) REVERT: C 218 GLU cc_start: 0.8826 (tp30) cc_final: 0.8562 (tp30) REVERT: C 219 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7735 (mt-10) REVERT: C 235 MET cc_start: 0.7974 (tpp) cc_final: 0.7511 (tmm) REVERT: D 329 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8828 (tt) REVERT: F 70 LEU cc_start: 0.8974 (tt) cc_final: 0.8538 (mp) REVERT: H 70 LEU cc_start: 0.8919 (tt) cc_final: 0.8528 (mp) outliers start: 26 outliers final: 21 residues processed: 207 average time/residue: 0.0812 time to fit residues: 20.8680 Evaluate side-chains 207 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain G residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN D 185 GLN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.127256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.104568 restraints weight = 12726.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.108013 restraints weight = 6523.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.110253 restraints weight = 4409.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.111701 restraints weight = 3475.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.112290 restraints weight = 2992.261| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5466 Z= 0.143 Angle : 0.679 7.500 7460 Z= 0.337 Chirality : 0.037 0.192 920 Planarity : 0.003 0.040 910 Dihedral : 3.518 18.275 748 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.85 % Allowed : 35.34 % Favored : 59.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.10 (0.32), residues: 682 helix: 3.06 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.55 (0.72), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 286 TYR 0.020 0.002 TYR D 317 PHE 0.021 0.001 PHE B 247 TRP 0.013 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5466) covalent geometry : angle 0.67886 ( 7460) hydrogen bonds : bond 0.04133 ( 519) hydrogen bonds : angle 3.27701 ( 1557) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.7551 (ttm) cc_final: 0.7143 (ttm) REVERT: B 221 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8816 (ttmt) REVERT: B 226 GLN cc_start: 0.8387 (pp30) cc_final: 0.7896 (pp30) REVERT: B 257 GLU cc_start: 0.7430 (mp0) cc_final: 0.7153 (mp0) REVERT: B 313 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6650 (m-30) REVERT: B 316 GLN cc_start: 0.7861 (pt0) cc_final: 0.7568 (tt0) REVERT: B 317 TYR cc_start: 0.9057 (t80) cc_final: 0.8696 (t80) REVERT: C 218 GLU cc_start: 0.8845 (tp30) cc_final: 0.8577 (tp30) REVERT: C 219 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7715 (mt-10) REVERT: C 235 MET cc_start: 0.8011 (tpp) cc_final: 0.7414 (tmm) REVERT: D 329 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8799 (tt) REVERT: F 70 LEU cc_start: 0.9005 (tt) cc_final: 0.8551 (mp) REVERT: H 70 LEU cc_start: 0.8925 (tt) cc_final: 0.8525 (mp) outliers start: 25 outliers final: 21 residues processed: 196 average time/residue: 0.0813 time to fit residues: 19.9030 Evaluate side-chains 202 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain G residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.0670 chunk 40 optimal weight: 0.0170 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 31 optimal weight: 0.0170 chunk 15 optimal weight: 0.8980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 304 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.127896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.105663 restraints weight = 12636.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.109132 restraints weight = 6546.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.111334 restraints weight = 4438.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.112783 restraints weight = 3523.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.113214 restraints weight = 3035.880| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5466 Z= 0.139 Angle : 0.686 8.978 7460 Z= 0.338 Chirality : 0.037 0.194 920 Planarity : 0.003 0.044 910 Dihedral : 3.508 16.643 748 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.27 % Allowed : 36.50 % Favored : 59.22 % 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: 4.02 (0.32), residues: 682 helix: 2.99 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.45 (0.74), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 286 TYR 0.015 0.001 TYR D 187 PHE 0.020 0.001 PHE B 247 TRP 0.010 0.001 TRP B 234 HIS 0.000 0.000 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5466) covalent geometry : angle 0.68646 ( 7460) hydrogen bonds : bond 0.04050 ( 519) hydrogen bonds : angle 3.26584 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1127.97 seconds wall clock time: 20 minutes 0.98 seconds (1200.98 seconds total)