Starting phenix.real_space_refine on Thu Mar 6 07:33:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x4s_22042/03_2025/6x4s_22042.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x4s_22042/03_2025/6x4s_22042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x4s_22042/03_2025/6x4s_22042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x4s_22042/03_2025/6x4s_22042.map" model { file = "/net/cci-nas-00/data/ceres_data/6x4s_22042/03_2025/6x4s_22042.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x4s_22042/03_2025/6x4s_22042.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} 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: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} 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: 4.04, per 1000 atoms: 0.75 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: 1.33 Conformation dependent library (CDL) restraints added in 670.9 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: 0.37 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: 1.33 Time building geometry restraints manager: 1.56 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 5466 Z= 0.427 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (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 TRP 0.025 0.002 TRP B 260 HIS 0.006 0.002 HIS C 195 PHE 0.011 0.002 PHE D 247 TYR 0.013 0.002 TYR C 258 ARG 0.002 0.000 ARG A 231 *********************** 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 : 0.559 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: 0.8606 (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: 0.7862 (ttm) REVERT: B 313 ASP cc_start: 0.8041 (t0) cc_final: 0.7809 (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: 0.8643 (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: 0.7624 (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: 0.8958 (t80) REVERT: C 263 MET cc_start: 0.8537 (mmm) cc_final: 0.8172 (tpp) REVERT: C 276 MET cc_start: 0.7603 (mtp) cc_final: 0.7226 (mmp) REVERT: C 317 TYR cc_start: 0.9096 (t80) cc_final: 0.8693 (t80) REVERT: C 328 GLU cc_start: 0.8459 (tt0) cc_final: 0.7985 (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: 0.7807 (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: 0.6368 (m110) REVERT: F 70 LEU cc_start: 0.9020 (tt) cc_final: 0.8566 (mp) REVERT: F 73 THR cc_start: 0.8314 (p) cc_final: 0.8104 (p) outliers start: 5 outliers final: 0 residues processed: 266 average time/residue: 0.2114 time to fit residues: 67.6962 Evaluate side-chains 207 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 315 ASN D 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.127570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103731 restraints weight = 13237.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.107281 restraints weight = 7035.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109578 restraints weight = 4858.269| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5466 Z= 0.231 Angle : 0.664 8.158 7460 Z= 0.334 Chirality : 0.037 0.177 920 Planarity : 0.004 0.029 910 Dihedral : 3.636 17.114 748 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.69 % Allowed : 28.35 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.32), residues: 682 helix: 2.98 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -3.00 (0.65), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 260 HIS 0.003 0.001 HIS C 195 PHE 0.010 0.001 PHE C 247 TYR 0.013 0.002 TYR B 279 ARG 0.007 0.001 ARG D 252 *********************** 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 247 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8565 (mtmt) REVERT: A 272 TYR cc_start: 0.8514 (t80) cc_final: 0.8185 (t80) REVERT: B 211 GLN cc_start: 0.8806 (mt0) cc_final: 0.8551 (mm-40) REVERT: B 243 MET cc_start: 0.7272 (mtp) cc_final: 0.6944 (mmt) REVERT: B 246 GLN cc_start: 0.9016 (tt0) cc_final: 0.8801 (tt0) REVERT: B 253 LEU cc_start: 0.8662 (mt) cc_final: 0.8438 (mp) REVERT: B 316 GLN cc_start: 0.7741 (pt0) cc_final: 0.7529 (tt0) REVERT: B 321 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8611 (mmmm) REVERT: C 221 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8858 (ttpt) REVERT: C 235 MET cc_start: 0.8013 (tpp) cc_final: 0.7729 (tmm) REVERT: C 247 PHE cc_start: 0.9297 (t80) cc_final: 0.9015 (t80) REVERT: D 213 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8572 (tm-30) REVERT: D 226 GLN cc_start: 0.8523 (pp30) cc_final: 0.8320 (pp30) REVERT: F 70 LEU cc_start: 0.8922 (tt) cc_final: 0.8427 (mp) REVERT: H 70 LEU cc_start: 0.8958 (tt) cc_final: 0.8545 (mp) outliers start: 19 outliers final: 12 residues processed: 237 average time/residue: 0.2030 time to fit residues: 59.2436 Evaluate side-chains 222 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 181 THR Chi-restraints excluded: chain D residue 198 GLN Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 271 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 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 198 GLN B 226 GLN B 246 GLN ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.126422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.103556 restraints weight = 13110.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107091 restraints weight = 6625.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.109321 restraints weight = 4468.766| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4070 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= 0.214 Angle : 0.601 7.716 7460 Z= 0.304 Chirality : 0.035 0.152 920 Planarity : 0.003 0.028 910 Dihedral : 3.514 15.706 748 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.05 % Allowed : 29.32 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.32), residues: 682 helix: 3.12 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.72 (0.79), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 260 HIS 0.003 0.001 HIS C 195 PHE 0.022 0.001 PHE B 247 TYR 0.016 0.002 TYR A 317 ARG 0.006 0.001 ARG A 286 *********************** 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 245 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8684 (mtmt) REVERT: A 272 TYR cc_start: 0.8501 (t80) cc_final: 0.8130 (t80) REVERT: B 243 MET cc_start: 0.7222 (mtp) cc_final: 0.7019 (mmt) REVERT: B 316 GLN cc_start: 0.7851 (pt0) cc_final: 0.7537 (tt0) REVERT: C 221 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8794 (ttmt) REVERT: C 226 GLN cc_start: 0.8850 (tt0) cc_final: 0.8629 (tt0) REVERT: C 235 MET cc_start: 0.7967 (tpp) cc_final: 0.7751 (tmm) REVERT: C 246 GLN cc_start: 0.9104 (tt0) cc_final: 0.8869 (tt0) REVERT: D 213 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8473 (tm-30) REVERT: D 226 GLN cc_start: 0.8594 (pp30) cc_final: 0.8367 (pp30) REVERT: F 70 LEU cc_start: 0.8959 (tt) cc_final: 0.8483 (mp) REVERT: H 70 LEU cc_start: 0.8983 (tt) cc_final: 0.8613 (mp) outliers start: 26 outliers final: 17 residues processed: 229 average time/residue: 0.2001 time to fit residues: 56.3034 Evaluate side-chains 227 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL 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 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 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 63 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 60 optimal weight: 0.0870 chunk 7 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 40 optimal weight: 0.0060 chunk 2 optimal weight: 0.8980 overall best weight: 0.1730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN B 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.129468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106479 restraints weight = 13451.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109966 restraints weight = 6915.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.112281 restraints weight = 4698.664| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5466 Z= 0.175 Angle : 0.599 7.627 7460 Z= 0.300 Chirality : 0.034 0.142 920 Planarity : 0.003 0.026 910 Dihedral : 3.482 15.563 748 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 4.47 % Allowed : 32.62 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.32), residues: 682 helix: 3.26 (0.20), residues: 632 sheet: None (None), residues: 0 loop : -2.93 (0.75), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.023 0.001 PHE C 247 TYR 0.018 0.002 TYR A 317 ARG 0.006 0.001 ARG A 286 *********************** 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 236 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.610 Fit side-chains REVERT: A 246 GLN cc_start: 0.8768 (tt0) cc_final: 0.8536 (tt0) REVERT: B 234 TRP cc_start: 0.8074 (t60) cc_final: 0.7725 (t60) REVERT: B 316 GLN cc_start: 0.7767 (pt0) cc_final: 0.7522 (tt0) REVERT: C 226 GLN cc_start: 0.8852 (tt0) cc_final: 0.8618 (tt0) REVERT: C 235 MET cc_start: 0.7916 (tpp) cc_final: 0.7659 (tmm) REVERT: C 246 GLN cc_start: 0.8949 (tt0) cc_final: 0.8708 (tt0) REVERT: C 272 TYR cc_start: 0.8377 (t80) cc_final: 0.8025 (t80) REVERT: D 213 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8489 (tm-30) REVERT: D 226 GLN cc_start: 0.8576 (pp30) cc_final: 0.8358 (pp30) REVERT: D 329 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8617 (tt) REVERT: F 70 LEU cc_start: 0.8950 (tt) cc_final: 0.8459 (mp) REVERT: H 70 LEU cc_start: 0.8956 (tt) cc_final: 0.8572 (mp) outliers start: 23 outliers final: 13 residues processed: 222 average time/residue: 0.2032 time to fit residues: 55.3968 Evaluate side-chains 213 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 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 51 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 315 ASN E 87 ASN G 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.128345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105775 restraints weight = 12199.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.109001 restraints weight = 6595.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.111057 restraints weight = 4579.643| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5466 Z= 0.242 Angle : 0.632 9.570 7460 Z= 0.314 Chirality : 0.036 0.165 920 Planarity : 0.003 0.022 910 Dihedral : 3.463 16.023 748 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.83 % Allowed : 31.84 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.32), residues: 682 helix: 3.17 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.97 (0.80), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.020 0.001 PHE C 247 TYR 0.020 0.002 TYR A 317 ARG 0.005 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: B 234 TRP cc_start: 0.8130 (t60) cc_final: 0.7828 (t60) REVERT: B 272 TYR cc_start: 0.8569 (t80) cc_final: 0.8194 (t80) REVERT: B 316 GLN cc_start: 0.7854 (pt0) cc_final: 0.7622 (tt0) REVERT: C 218 GLU cc_start: 0.8663 (tp30) cc_final: 0.8434 (tp30) REVERT: C 226 GLN cc_start: 0.8785 (tt0) cc_final: 0.8510 (tt0) REVERT: C 235 MET cc_start: 0.7909 (tpp) cc_final: 0.7705 (tmm) REVERT: C 272 TYR cc_start: 0.8411 (t80) cc_final: 0.8196 (t80) REVERT: D 329 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8711 (tt) REVERT: F 70 LEU cc_start: 0.8993 (tt) cc_final: 0.8479 (mp) REVERT: H 70 LEU cc_start: 0.8962 (tt) cc_final: 0.8511 (mp) outliers start: 30 outliers final: 20 residues processed: 220 average time/residue: 0.1982 time to fit residues: 53.8237 Evaluate side-chains 216 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 254 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 267 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 Chi-restraints excluded: chain G residue 90 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 24 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.127082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103888 restraints weight = 13007.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.107266 restraints weight = 6788.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109539 restraints weight = 4667.852| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5466 Z= 0.222 Angle : 0.652 9.728 7460 Z= 0.321 Chirality : 0.035 0.157 920 Planarity : 0.003 0.025 910 Dihedral : 3.449 18.367 748 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 5.63 % Allowed : 33.20 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.32), residues: 682 helix: 3.12 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.91 (0.81), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.022 0.001 PHE B 247 TYR 0.018 0.001 TYR A 317 ARG 0.006 0.001 ARG A 230 *********************** 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 234 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: B 234 TRP cc_start: 0.8138 (t60) cc_final: 0.7837 (t60) REVERT: B 316 GLN cc_start: 0.7903 (pt0) cc_final: 0.7615 (tt0) REVERT: C 226 GLN cc_start: 0.8869 (tt0) cc_final: 0.8611 (tt0) REVERT: C 235 MET cc_start: 0.8008 (tpp) cc_final: 0.7560 (tmm) REVERT: C 243 MET cc_start: 0.8213 (ttm) cc_final: 0.7632 (ttm) REVERT: D 263 MET cc_start: 0.7832 (ttp) cc_final: 0.7575 (ttp) REVERT: D 329 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8756 (tt) REVERT: F 70 LEU cc_start: 0.8995 (tt) cc_final: 0.8508 (mp) REVERT: H 70 LEU cc_start: 0.8960 (tt) cc_final: 0.8551 (mp) outliers start: 29 outliers final: 26 residues processed: 217 average time/residue: 0.1931 time to fit residues: 51.7264 Evaluate side-chains 224 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 263 MET 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 232 SER Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 274 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 253 LEU Chi-restraints excluded: chain D residue 267 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 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 63 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.125474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102297 restraints weight = 12988.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105764 restraints weight = 6792.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107913 restraints weight = 4696.593| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5466 Z= 0.246 Angle : 0.643 7.920 7460 Z= 0.322 Chirality : 0.036 0.156 920 Planarity : 0.003 0.025 910 Dihedral : 3.419 17.842 748 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 11.41 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.32), residues: 682 helix: 3.07 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.97 (0.80), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.021 0.001 PHE B 247 TYR 0.020 0.002 TYR A 258 ARG 0.007 0.001 ARG A 286 *********************** 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 230 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: B 234 TRP cc_start: 0.8196 (t60) cc_final: 0.7877 (t60) REVERT: B 313 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6925 (m-30) REVERT: B 316 GLN cc_start: 0.7994 (pt0) cc_final: 0.7727 (tt0) REVERT: C 226 GLN cc_start: 0.8840 (tt0) cc_final: 0.8581 (tt0) REVERT: C 235 MET cc_start: 0.8052 (tpp) cc_final: 0.7590 (tmm) REVERT: D 329 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8794 (tt) REVERT: F 70 LEU cc_start: 0.9029 (tt) cc_final: 0.8558 (mp) REVERT: H 70 LEU cc_start: 0.8981 (tt) cc_final: 0.8590 (mp) outliers start: 31 outliers final: 27 residues processed: 213 average time/residue: 0.1992 time to fit residues: 52.3197 Evaluate side-chains 222 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 253 LEU 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 C residue 244 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 274 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 253 LEU 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 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 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.125407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.102495 restraints weight = 12833.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.105916 restraints weight = 6671.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.108167 restraints weight = 4613.741| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5466 Z= 0.241 Angle : 0.669 7.683 7460 Z= 0.334 Chirality : 0.036 0.162 920 Planarity : 0.003 0.026 910 Dihedral : 3.435 16.588 748 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.05 % Allowed : 33.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.03 (0.32), residues: 682 helix: 2.96 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.84 (0.82), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 260 HIS 0.001 0.000 HIS A 304 PHE 0.019 0.001 PHE B 247 TYR 0.016 0.002 TYR A 317 ARG 0.007 0.001 ARG A 230 *********************** 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 223 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.620 Fit side-chains REVERT: A 321 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8498 (ttmm) REVERT: B 313 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6860 (m-30) REVERT: C 213 GLU cc_start: 0.8910 (tp30) cc_final: 0.8675 (tp30) REVERT: C 219 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7812 (mt-10) REVERT: C 226 GLN cc_start: 0.8837 (tt0) cc_final: 0.8571 (tt0) REVERT: C 235 MET cc_start: 0.7976 (tpp) cc_final: 0.7516 (tmm) REVERT: D 329 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8769 (tt) REVERT: F 70 LEU cc_start: 0.9023 (tt) cc_final: 0.8579 (mp) REVERT: H 70 LEU cc_start: 0.8987 (tt) cc_final: 0.8600 (mp) outliers start: 26 outliers final: 23 residues processed: 208 average time/residue: 0.2009 time to fit residues: 51.4437 Evaluate side-chains 220 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 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 245 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 237 TRP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 267 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 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 54 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.0020 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 46 optimal weight: 0.0040 chunk 64 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 overall best weight: 0.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.128116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105932 restraints weight = 12185.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109253 restraints weight = 6334.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.111474 restraints weight = 4328.220| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5466 Z= 0.188 Angle : 0.670 8.280 7460 Z= 0.331 Chirality : 0.036 0.173 920 Planarity : 0.003 0.025 910 Dihedral : 3.527 15.399 748 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.88 % Allowed : 35.15 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.32), residues: 682 helix: 2.98 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.62 (0.79), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 234 HIS 0.000 0.000 HIS C 195 PHE 0.024 0.001 PHE B 247 TYR 0.015 0.002 TYR A 317 ARG 0.006 0.001 ARG A 286 *********************** 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 225 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.612 Fit side-chains REVERT: A 246 GLN cc_start: 0.8876 (tt0) cc_final: 0.8651 (tm-30) REVERT: B 221 LYS cc_start: 0.9012 (ttpp) cc_final: 0.8807 (ttmt) REVERT: B 226 GLN cc_start: 0.8223 (pp30) cc_final: 0.7836 (pp30) REVERT: B 234 TRP cc_start: 0.8083 (t60) cc_final: 0.7747 (t60) REVERT: B 243 MET cc_start: 0.7030 (mmt) cc_final: 0.6793 (mmt) REVERT: B 276 MET cc_start: 0.8108 (mmm) cc_final: 0.7898 (mmm) REVERT: B 313 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: B 317 TYR cc_start: 0.9128 (t80) cc_final: 0.8806 (t80) REVERT: C 213 GLU cc_start: 0.8904 (tp30) cc_final: 0.8659 (tp30) REVERT: C 219 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7840 (mt-10) REVERT: C 226 GLN cc_start: 0.8822 (tt0) cc_final: 0.8567 (tt0) REVERT: C 235 MET cc_start: 0.7990 (tpp) cc_final: 0.7447 (tmm) REVERT: D 329 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8775 (tt) REVERT: F 70 LEU cc_start: 0.8993 (tt) cc_final: 0.8528 (mp) REVERT: H 70 LEU cc_start: 0.8934 (tt) cc_final: 0.8547 (mp) outliers start: 20 outliers final: 15 residues processed: 214 average time/residue: 0.2014 time to fit residues: 52.9679 Evaluate side-chains 211 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 51 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.125632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102853 restraints weight = 12830.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106231 restraints weight = 6797.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.108423 restraints weight = 4688.922| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5466 Z= 0.256 Angle : 0.711 8.924 7460 Z= 0.354 Chirality : 0.038 0.182 920 Planarity : 0.003 0.041 910 Dihedral : 3.487 17.168 748 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.27 % Allowed : 34.17 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.32), residues: 682 helix: 2.92 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.71 (0.76), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 PHE 0.023 0.001 PHE B 247 TYR 0.020 0.002 TYR D 317 ARG 0.009 0.001 ARG A 286 ********************** 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 215 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8992 (tt0) cc_final: 0.8621 (tm-30) REVERT: A 321 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8502 (ttmm) REVERT: B 221 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8816 (ttmt) REVERT: B 243 MET cc_start: 0.7051 (mmt) cc_final: 0.6813 (mmt) REVERT: B 313 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6777 (m-30) REVERT: C 219 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7795 (mt-10) REVERT: C 226 GLN cc_start: 0.8819 (tt0) cc_final: 0.8599 (tt0) REVERT: C 235 MET cc_start: 0.8064 (tpp) cc_final: 0.7565 (tmm) REVERT: D 231 ARG cc_start: 0.8152 (ttt90) cc_final: 0.7875 (tmm-80) REVERT: D 329 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8801 (tt) REVERT: F 70 LEU cc_start: 0.8994 (tt) cc_final: 0.8548 (mp) REVERT: H 70 LEU cc_start: 0.8951 (tt) cc_final: 0.8568 (mp) outliers start: 22 outliers final: 15 residues processed: 205 average time/residue: 0.1966 time to fit residues: 49.8199 Evaluate side-chains 206 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 237 TRP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 237 TRP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain 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 267 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain E residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.126568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.103730 restraints weight = 12951.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107143 restraints weight = 6698.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109495 restraints weight = 4569.154| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5466 Z= 0.230 Angle : 0.684 8.197 7460 Z= 0.342 Chirality : 0.037 0.184 920 Planarity : 0.003 0.043 910 Dihedral : 3.518 18.220 748 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.50 % Allowed : 35.53 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.32), residues: 682 helix: 2.92 (0.20), residues: 630 sheet: None (None), residues: 0 loop : -2.54 (0.74), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 234 HIS 0.001 0.000 HIS A 304 PHE 0.024 0.001 PHE B 247 TYR 0.021 0.002 TYR B 317 ARG 0.010 0.001 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2175.84 seconds wall clock time: 38 minutes 27.31 seconds (2307.31 seconds total)