Starting phenix.real_space_refine on Thu Sep 10 23:27:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x4s_22042/09_2026/6x4s_22042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x4s_22042/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6x4s_22042/09_2026/6x4s_22042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x4s_22042/09_2026/6x4s_22042.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6x4s_22042/09_2026/6x4s_22042.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x4s_22042/09_2026/6x4s_22042.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x4s_22042/09_2026/6x4s_22042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x4s_22042/09_2026/6x4s_22042.map" } 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-2.2.1-6174/lib/python3.11/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: 1.39, 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: 0.49 Conformation dependent library (CDL) restraints added in 200.0 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: 0.69 Time building geometry restraints manager: 0.66 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.320 Find NCS groups from input model: 0.150 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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/Z covalent geometry : bond 0.00653 / 0.29 ( 5466) covalent geometry : angle 0.76784 / 0.40 ( 7460) hydrogen bonds : bond 0.10803 / 7.20 ( 519) hydrogen bonds : angle 4.68424 / 3.37 ( 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 : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 0.7337 (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: 0.8270 (tt0) REVERT: C 229 ASN cc_start: 0.8826 (m-40) cc_final: 0.8593 (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: 0.7225 (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: 0.8002 (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: 0.8511 (mp) outliers start: 5 outliers final: 0 residues processed: 266 average time/residue: 0.0934 time to fit residues: 30.4259 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 : 0.216 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.125997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102963 restraints weight = 13339.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106469 restraints weight = 6903.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108732 restraints weight = 4702.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109736 restraints weight = 3741.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.110892 restraints weight = 3310.870| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5466 Z= 0.174 Angle : 0.676 8.025 7460 Z= 0.342 Chirality : 0.037 0.184 920 Planarity : 0.004 0.029 910 Dihedral : 3.628 17.209 748 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.85 % Allowed : 27.57 % Favored : 67.57 % 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 : -2.95 (0.65), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 231 TYR 0.014 0.002 TYR C 187 PHE 0.011 0.001 PHE C 247 TRP 0.016 0.002 TRP A 260 HIS 0.004 0.001 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 5466) covalent geometry : angle 0.67578 / 0.34 ( 7460) hydrogen bonds : bond 0.04857 / 3.39 ( 519) hydrogen bonds : angle 3.29835 / 2.36 ( 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 243 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8708 (mtmt) REVERT: A 272 TYR cc_start: 0.8565 (t80) cc_final: 0.8250 (t80) REVERT: B 243 MET cc_start: 0.7228 (mtp) cc_final: 0.7020 (mmt) REVERT: B 246 GLN cc_start: 0.9005 (tt0) cc_final: 0.8798 (tt0) REVERT: B 253 LEU cc_start: 0.8638 (mt) cc_final: 0.8412 (mp) REVERT: B 316 GLN cc_start: 0.7722 (pt0) cc_final: 0.7490 (tt0) REVERT: C 221 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8907 (ttpt) REVERT: C 235 MET cc_start: 0.7977 (tpp) cc_final: 0.7747 (tmm) REVERT: D 213 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8535 (tm-30) REVERT: F 70 LEU cc_start: 0.8889 (tt) cc_final: 0.8379 (mp) REVERT: H 70 LEU cc_start: 0.8863 (tt) cc_final: 0.8444 (mp) outliers start: 25 outliers final: 17 residues processed: 231 average time/residue: 0.0870 time to fit residues: 24.7667 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 : 0.210 ------------------------------------------------------------------------------- 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 C residue 285 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: 0.6980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN B 246 GLN C 229 ASN C 315 ASN E 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.124860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101719 restraints weight = 13228.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.105262 restraints weight = 6667.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107490 restraints weight = 4521.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.108867 restraints weight = 3595.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109239 restraints weight = 3134.503| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4184 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 : 0.610 7.906 7460 Z= 0.310 Chirality : 0.035 0.144 920 Planarity : 0.003 0.028 910 Dihedral : 3.510 16.004 748 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.24 % Allowed : 28.93 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.21 (0.32), residues: 682 helix: 3.14 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -2.91 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.016 0.002 TYR A 317 PHE 0.022 0.001 PHE B 247 TRP 0.013 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 5466) covalent geometry : angle 0.61011 / 0.31 ( 7460) hydrogen bonds : bond 0.04566 / 3.20 ( 519) hydrogen bonds : angle 3.16874 / 2.23 ( 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 244 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8707 (ttmt) REVERT: A 235 MET cc_start: 0.8388 (tpp) cc_final: 0.8170 (tpp) REVERT: A 272 TYR cc_start: 0.8535 (t80) cc_final: 0.8219 (t80) REVERT: B 226 GLN cc_start: 0.8243 (pp30) cc_final: 0.7849 (pp30) REVERT: B 243 MET cc_start: 0.7369 (mtp) cc_final: 0.7046 (mmt) REVERT: B 316 GLN cc_start: 0.7791 (pt0) cc_final: 0.7501 (tt0) REVERT: C 235 MET cc_start: 0.8003 (tpp) cc_final: 0.7728 (tmm) REVERT: C 246 GLN cc_start: 0.9151 (tt0) cc_final: 0.8934 (tt0) REVERT: C 263 MET cc_start: 0.8398 (tpp) cc_final: 0.8114 (tpp) REVERT: D 213 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8540 (tm-30) REVERT: D 326 LYS cc_start: 0.8971 (tppt) cc_final: 0.8767 (tppt) REVERT: F 70 LEU cc_start: 0.9015 (tt) cc_final: 0.8532 (mp) REVERT: H 70 LEU cc_start: 0.8865 (tt) cc_final: 0.8557 (mp) outliers start: 27 outliers final: 19 residues processed: 228 average time/residue: 0.0858 time to fit residues: 24.3709 Evaluate side-chains 225 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 254 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 64 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 0.0000 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.128236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105194 restraints weight = 12168.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.108512 restraints weight = 6470.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110626 restraints weight = 4485.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.111779 restraints weight = 3592.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.112736 restraints weight = 3168.043| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5466 Z= 0.140 Angle : 0.596 7.669 7460 Z= 0.300 Chirality : 0.035 0.138 920 Planarity : 0.003 0.023 910 Dihedral : 3.486 15.172 748 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.47 % Allowed : 32.23 % 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: 4.31 (0.32), residues: 682 helix: 3.16 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.69 (0.78), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 286 TYR 0.017 0.002 TYR A 317 PHE 0.019 0.001 PHE B 247 TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 5466) covalent geometry : angle 0.59643 / 0.30 ( 7460) hydrogen bonds : bond 0.04346 / 3.04 ( 519) hydrogen bonds : angle 3.05771 / 2.16 ( 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 228 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8295 (pp30) cc_final: 0.7857 (pp30) REVERT: B 234 TRP cc_start: 0.8167 (t60) cc_final: 0.7803 (t60) REVERT: B 316 GLN cc_start: 0.7856 (pt0) cc_final: 0.7613 (tt0) REVERT: C 226 GLN cc_start: 0.8771 (tt0) cc_final: 0.8557 (tt0) REVERT: C 235 MET cc_start: 0.7977 (tpp) cc_final: 0.7658 (tmm) REVERT: C 246 GLN cc_start: 0.9114 (tt0) cc_final: 0.8877 (tt0) REVERT: C 263 MET cc_start: 0.8399 (tpp) cc_final: 0.8197 (tpp) REVERT: D 326 LYS cc_start: 0.9016 (tppt) cc_final: 0.8801 (tppt) REVERT: D 329 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8655 (tt) REVERT: F 70 LEU cc_start: 0.8993 (tt) cc_final: 0.8453 (mp) REVERT: H 70 LEU cc_start: 0.8923 (tt) cc_final: 0.8546 (mp) outliers start: 23 outliers final: 17 residues processed: 214 average time/residue: 0.0854 time to fit residues: 22.6457 Evaluate side-chains 211 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 237 TRP Chi-restraints excluded: chain D residue 254 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=3.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 318 ASN ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.126165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103129 restraints weight = 12540.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106409 restraints weight = 6650.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108455 restraints weight = 4594.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.109748 restraints weight = 3690.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.110652 restraints weight = 3222.896| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5466 Z= 0.153 Angle : 0.621 8.575 7460 Z= 0.311 Chirality : 0.035 0.170 920 Planarity : 0.003 0.023 910 Dihedral : 3.408 15.025 748 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 6.02 % Allowed : 32.62 % Favored : 61.36 % 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: 4.20 (0.32), residues: 682 helix: 3.07 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.69 (0.81), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 286 TYR 0.019 0.002 TYR A 317 PHE 0.022 0.001 PHE B 247 TRP 0.012 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 5466) covalent geometry : angle 0.62068 / 0.31 ( 7460) hydrogen bonds : bond 0.04345 / 3.02 ( 519) hydrogen bonds : angle 3.09333 / 2.18 ( 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 234 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8373 (pp30) cc_final: 0.7907 (pp30) REVERT: B 234 TRP cc_start: 0.8168 (t60) cc_final: 0.7897 (t60) REVERT: B 316 GLN cc_start: 0.7896 (pt0) cc_final: 0.7656 (tt0) REVERT: B 321 LYS cc_start: 0.9123 (mmtp) cc_final: 0.8917 (mmtm) REVERT: C 235 MET cc_start: 0.8026 (tpp) cc_final: 0.7680 (tmm) REVERT: C 246 GLN cc_start: 0.9128 (tt0) cc_final: 0.8903 (tt0) REVERT: D 326 LYS cc_start: 0.9087 (tppt) cc_final: 0.8864 (tppt) REVERT: D 329 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8660 (tt) REVERT: F 70 LEU cc_start: 0.8961 (tt) cc_final: 0.8468 (mp) REVERT: H 70 LEU cc_start: 0.8933 (tt) cc_final: 0.8590 (mp) outliers start: 31 outliers final: 21 residues processed: 216 average time/residue: 0.0809 time to fit residues: 21.9145 Evaluate side-chains 220 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 267 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 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: 0.7980 chunk 57 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.0040 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS ** 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 = 0.3983 r_free = 0.3983 target = 0.126785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103962 restraints weight = 13279.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107427 restraints weight = 6891.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.109741 restraints weight = 4722.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111178 restraints weight = 3748.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.111406 restraints weight = 3240.455| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5466 Z= 0.137 Angle : 0.617 7.608 7460 Z= 0.306 Chirality : 0.035 0.163 920 Planarity : 0.003 0.028 910 Dihedral : 3.410 15.709 748 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.44 % Allowed : 31.84 % Favored : 62.72 % 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: 4.17 (0.32), residues: 682 helix: 3.04 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.61 (0.83), residues: 44 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 0.012 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 5466) covalent geometry : angle 0.61748 / 0.31 ( 7460) hydrogen bonds : bond 0.04194 / 2.91 ( 519) hydrogen bonds : angle 3.15151 / 2.21 ( 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 230 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8362 (pp30) cc_final: 0.7868 (pp30) REVERT: B 234 TRP cc_start: 0.8137 (t60) cc_final: 0.7807 (t60) REVERT: B 313 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: B 316 GLN cc_start: 0.7887 (pt0) cc_final: 0.7606 (tt0) REVERT: B 321 LYS cc_start: 0.9042 (mmtp) cc_final: 0.8829 (mmtm) REVERT: C 235 MET cc_start: 0.8086 (tpp) cc_final: 0.7674 (tmm) REVERT: C 246 GLN cc_start: 0.9132 (tt0) cc_final: 0.8920 (tt0) REVERT: D 326 LYS cc_start: 0.9072 (tppt) cc_final: 0.8866 (tppt) REVERT: D 329 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8733 (tt) REVERT: F 70 LEU cc_start: 0.8996 (tt) cc_final: 0.8526 (mp) REVERT: H 70 LEU cc_start: 0.8952 (tt) cc_final: 0.8607 (mp) outliers start: 28 outliers final: 23 residues processed: 211 average time/residue: 0.0829 time to fit residues: 21.9797 Evaluate side-chains 217 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 267 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 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 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: 0.5980 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.124894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101834 restraints weight = 13277.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.105311 restraints weight = 6904.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.107535 restraints weight = 4744.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.108893 restraints weight = 3791.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109460 restraints weight = 3298.539| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5466 Z= 0.154 Angle : 0.637 10.830 7460 Z= 0.317 Chirality : 0.036 0.153 920 Planarity : 0.003 0.027 910 Dihedral : 3.391 15.625 748 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.83 % Allowed : 32.43 % Favored : 61.75 % 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 : -2.58 (0.73), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 286 TYR 0.016 0.002 TYR A 317 PHE 0.018 0.001 PHE B 247 TRP 0.009 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 5466) covalent geometry : angle 0.63713 / 0.32 ( 7460) hydrogen bonds : bond 0.04280 / 2.98 ( 519) hydrogen bonds : angle 3.15291 / 2.22 ( 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 228 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8398 (pp30) cc_final: 0.7894 (pp30) REVERT: B 313 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7019 (m-30) REVERT: B 316 GLN cc_start: 0.7969 (pt0) cc_final: 0.7680 (tt0) REVERT: B 321 LYS cc_start: 0.9075 (mmtp) cc_final: 0.8844 (mmtm) REVERT: C 219 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7887 (mt-10) REVERT: C 235 MET cc_start: 0.8092 (tpp) cc_final: 0.7613 (tmm) REVERT: D 329 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8745 (tt) REVERT: F 70 LEU cc_start: 0.9051 (tt) cc_final: 0.8561 (mp) REVERT: H 70 LEU cc_start: 0.8995 (tt) cc_final: 0.8575 (mp) outliers start: 30 outliers final: 26 residues processed: 209 average time/residue: 0.0816 time to fit residues: 21.2278 Evaluate side-chains 220 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 267 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 0.0370 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN D 246 GLN G 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.126061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.103380 restraints weight = 12999.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.106813 restraints weight = 6893.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108990 restraints weight = 4760.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.110385 restraints weight = 3803.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110805 restraints weight = 3296.132| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5466 Z= 0.142 Angle : 0.638 10.702 7460 Z= 0.315 Chirality : 0.036 0.157 920 Planarity : 0.003 0.024 910 Dihedral : 3.394 15.402 748 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 6.02 % Allowed : 33.40 % Favored : 60.58 % 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: 4.07 (0.32), residues: 682 helix: 3.04 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.61 (0.76), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 286 TYR 0.017 0.002 TYR A 317 PHE 0.023 0.001 PHE B 247 TRP 0.011 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5466) covalent geometry : angle 0.63813 / 0.32 ( 7460) hydrogen bonds : bond 0.04201 / 2.93 ( 519) hydrogen bonds : angle 3.15130 / 2.21 ( 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 226 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8391 (pp30) cc_final: 0.7927 (pp30) REVERT: B 234 TRP cc_start: 0.8164 (t60) cc_final: 0.7832 (t60) REVERT: B 313 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.6912 (m-30) REVERT: B 316 GLN cc_start: 0.7870 (pt0) cc_final: 0.7586 (tt0) REVERT: B 321 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8854 (mmtm) REVERT: C 219 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7878 (mt-10) REVERT: C 235 MET cc_start: 0.8078 (tpp) cc_final: 0.7580 (tmm) REVERT: C 246 GLN cc_start: 0.9235 (tt0) cc_final: 0.8892 (tt0) REVERT: D 213 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 329 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8718 (tt) REVERT: F 70 LEU cc_start: 0.9012 (tt) cc_final: 0.8557 (mp) REVERT: H 70 LEU cc_start: 0.8898 (tt) cc_final: 0.8562 (mp) outliers start: 31 outliers final: 27 residues processed: 205 average time/residue: 0.0800 time to fit residues: 20.6680 Evaluate side-chains 220 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 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 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 266 VAL Chi-restraints excluded: chain D residue 267 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 G residue 90 ASN 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: 0.4980 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 63 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 2 optimal weight: 0.0010 overall best weight: 0.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 315 ASN D 246 GLN G 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.127471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104639 restraints weight = 12913.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108229 restraints weight = 6754.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110455 restraints weight = 4628.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.111877 restraints weight = 3700.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.112430 restraints weight = 3213.073| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5466 Z= 0.134 Angle : 0.653 10.273 7460 Z= 0.319 Chirality : 0.035 0.186 920 Planarity : 0.003 0.041 910 Dihedral : 3.440 15.630 748 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.66 % Allowed : 35.53 % 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: 4.06 (0.32), residues: 682 helix: 3.03 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.58 (0.77), 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 0.011 0.001 TRP B 234 HIS 0.000 0.000 HIS C 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 5466) covalent geometry : angle 0.65302 / 0.32 ( 7460) hydrogen bonds : bond 0.04065 / 2.84 ( 519) hydrogen bonds : angle 3.09903 / 2.18 ( 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 218 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8807 (mmmm) cc_final: 0.8298 (ttmm) REVERT: B 226 GLN cc_start: 0.8358 (pp30) cc_final: 0.7916 (pp30) REVERT: B 243 MET cc_start: 0.7009 (mmt) cc_final: 0.6743 (mmt) REVERT: B 313 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: B 316 GLN cc_start: 0.7824 (pt0) cc_final: 0.7565 (tt0) REVERT: C 219 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7836 (mt-10) REVERT: C 235 MET cc_start: 0.8011 (tpp) cc_final: 0.7540 (tmm) REVERT: C 246 GLN cc_start: 0.9203 (tt0) cc_final: 0.8863 (tt0) REVERT: C 263 MET cc_start: 0.8156 (tpp) cc_final: 0.7815 (tpp) REVERT: D 329 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8746 (tt) REVERT: F 70 LEU cc_start: 0.8974 (tt) cc_final: 0.8543 (mp) REVERT: H 70 LEU cc_start: 0.8873 (tt) cc_final: 0.8563 (mp) outliers start: 24 outliers final: 14 residues processed: 203 average time/residue: 0.0758 time to fit residues: 19.4718 Evaluate side-chains 201 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP 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: 0.6980 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 0.2980 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 57 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 overall best weight: 0.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 ASN A 323 GLN D 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.128177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.105293 restraints weight = 13310.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.108823 restraints weight = 7034.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111174 restraints weight = 4841.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.112607 restraints weight = 3846.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113319 restraints weight = 3325.773| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5556 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= 0.135 Angle : 0.671 9.309 7460 Z= 0.328 Chirality : 0.036 0.191 920 Planarity : 0.003 0.042 910 Dihedral : 3.446 15.666 748 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 4.27 % Allowed : 36.31 % Favored : 59.42 % 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 : -2.56 (0.75), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 286 TYR 0.017 0.001 TYR A 317 PHE 0.021 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/Z covalent geometry : bond 0.00285 / 0.13 ( 5466) covalent geometry : angle 0.67067 / 0.33 ( 7460) hydrogen bonds : bond 0.03999 / 2.79 ( 519) hydrogen bonds : angle 3.13512 / 2.21 ( 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 214 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: B 226 GLN cc_start: 0.8370 (pp30) cc_final: 0.7865 (pp30) REVERT: B 243 MET cc_start: 0.7075 (mmt) cc_final: 0.6811 (mmt) REVERT: B 313 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6830 (m-30) REVERT: B 316 GLN cc_start: 0.7809 (pt0) cc_final: 0.7562 (tt0) REVERT: B 317 TYR cc_start: 0.9116 (t80) cc_final: 0.8824 (t80) REVERT: B 321 LYS cc_start: 0.9006 (mmtp) cc_final: 0.8787 (mmtp) REVERT: C 219 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7789 (mt-10) REVERT: C 235 MET cc_start: 0.7994 (tpp) cc_final: 0.7448 (tmm) REVERT: C 246 GLN cc_start: 0.9178 (tt0) cc_final: 0.8852 (tt0) REVERT: D 329 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8765 (tt) REVERT: F 70 LEU cc_start: 0.8995 (tt) cc_final: 0.8548 (mp) REVERT: H 70 LEU cc_start: 0.8881 (tt) cc_final: 0.8560 (mp) outliers start: 22 outliers final: 15 residues processed: 202 average time/residue: 0.0785 time to fit residues: 19.9319 Evaluate side-chains 205 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 323 GLN 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 274 THR Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 262 ILE 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: 0.8980 chunk 32 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN D 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.127383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104819 restraints weight = 13234.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108387 restraints weight = 6912.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110657 restraints weight = 4738.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111758 restraints weight = 3774.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.112937 restraints weight = 3315.190| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.200 5466 Z= 0.240 Angle : 1.132 59.182 7460 Z= 0.678 Chirality : 0.043 0.436 920 Planarity : 0.003 0.040 910 Dihedral : 3.551 25.317 748 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.69 % Allowed : 36.70 % Favored : 59.61 % Cbeta Deviations : 0.15 % 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: 4.01 (0.32), residues: 682 helix: 3.00 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.58 (0.74), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 286 TYR 0.016 0.002 TYR A 317 PHE 0.021 0.001 PHE B 247 TRP 0.009 0.001 TRP B 234 HIS 0.000 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 ( 5466) covalent geometry : angle 1.13194 / 0.68 ( 7460) hydrogen bonds : bond 0.04068 / 2.85 ( 519) hydrogen bonds : angle 3.15826 / 2.23 ( 1557) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1159.72 seconds wall clock time: 21 minutes 14.93 seconds (1274.93 seconds total)