Starting phenix.real_space_refine on Wed Sep 17 14:09:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwp_38740/09_2025/8xwp_38740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwp_38740/09_2025/8xwp_38740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwp_38740/09_2025/8xwp_38740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwp_38740/09_2025/8xwp_38740.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwp_38740/09_2025/8xwp_38740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwp_38740/09_2025/8xwp_38740.cif" } resolution = 3.21 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 5795 2.51 5 N 1528 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9076 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2404 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.47, per 1000 atoms: 0.27 Number of scatterers: 9076 At special positions: 0 Unit cell: (119, 120.19, 115.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1683 8.00 N 1528 7.00 C 5795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.04 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 372.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2182 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.846A pdb=" N VAL R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 161 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 170 through 205 Proline residue: R 178 - end of helix removed outlier: 4.779A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 238 removed outlier: 3.848A pdb=" N VAL R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) Proline residue: R 235 - end of helix Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.502A pdb=" N GLN R 267 " --> pdb=" O THR R 263 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 282 removed outlier: 3.524A pdb=" N TRP R 276 " --> pdb=" O ALA R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 Processing helix chain 'R' and resid 313 through 349 removed outlier: 3.561A pdb=" N PHE R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 356 through 388 removed outlier: 4.037A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 399 Processing helix chain 'L' and resid 10 through 18 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.972A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.642A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.550A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.590A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 243 removed outlier: 4.033A pdb=" N LEU R 256 " --> pdb=" O ASP R 241 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE R 254 " --> pdb=" O ILE R 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 246 through 247 Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.587A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.556A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.563A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.669A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.597A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.390A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.629A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.428A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.512A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.623A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.491A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1236 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: 1.66 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2906 1.35 - 1.47: 2274 1.47 - 1.59: 3988 1.59 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 9266 Sorted by residual: bond pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.21e-02 6.83e+03 2.57e+00 bond pdb=" CA VAL R 177 " pdb=" CB VAL R 177 " ideal model delta sigma weight residual 1.539 1.546 -0.007 5.40e-03 3.43e+04 1.80e+00 bond pdb=" CB ARG R 208 " pdb=" CG ARG R 208 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.90e-01 bond pdb=" CA TRP R 206 " pdb=" CB TRP R 206 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.21e-02 6.83e+03 8.55e-01 bond pdb=" C MET D 180 " pdb=" N SER D 181 " ideal model delta sigma weight residual 1.332 1.321 0.011 1.40e-02 5.10e+03 6.67e-01 ... (remaining 9261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 12290 1.30 - 2.61: 202 2.61 - 3.91: 45 3.91 - 5.21: 15 5.21 - 6.51: 3 Bond angle restraints: 12555 Sorted by residual: angle pdb=" N MET L 7 " pdb=" CA MET L 7 " pdb=" C MET L 7 " ideal model delta sigma weight residual 114.04 110.50 3.54 1.24e+00 6.50e-01 8.17e+00 angle pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " pdb=" CG ARG R 208 " ideal model delta sigma weight residual 114.10 119.68 -5.58 2.00e+00 2.50e-01 7.78e+00 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 125.57 -4.03 1.91e+00 2.74e-01 4.45e+00 angle pdb=" N VAL R 234 " pdb=" CA VAL R 234 " pdb=" C VAL R 234 " ideal model delta sigma weight residual 108.88 113.33 -4.45 2.16e+00 2.14e-01 4.25e+00 angle pdb=" C GLY A 42 " pdb=" N GLU A 43 " pdb=" CA GLU A 43 " ideal model delta sigma weight residual 121.54 125.36 -3.82 1.91e+00 2.74e-01 4.00e+00 ... (remaining 12550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5128 17.74 - 35.47: 308 35.47 - 53.21: 64 53.21 - 70.95: 14 70.95 - 88.69: 3 Dihedral angle restraints: 5517 sinusoidal: 2139 harmonic: 3378 Sorted by residual: dihedral pdb=" CB CYS R 174 " pdb=" SG CYS R 174 " pdb=" SG CYS R 255 " pdb=" CB CYS R 255 " ideal model delta sinusoidal sigma weight residual -86.00 -143.30 57.30 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 123.99 -30.99 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA ARG R 208 " pdb=" C ARG R 208 " pdb=" N ILE R 209 " pdb=" CA ILE R 209 " ideal model delta harmonic sigma weight residual -180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 840 0.025 - 0.051: 365 0.051 - 0.076: 124 0.076 - 0.102: 69 0.102 - 0.127: 35 Chirality restraints: 1433 Sorted by residual: chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE D 204 " pdb=" N ILE D 204 " pdb=" C ILE D 204 " pdb=" CB ILE D 204 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 1430 not shown) Planarity restraints: 1579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 234 " -0.032 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO R 235 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO R 235 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 235 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 135 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO R 136 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 136 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 136 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 167 " 0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO R 168 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " 0.016 5.00e-02 4.00e+02 ... (remaining 1576 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 243 2.70 - 3.25: 9098 3.25 - 3.80: 14499 3.80 - 4.35: 19007 4.35 - 4.90: 31717 Nonbonded interactions: 74564 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.144 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.155 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.179 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.183 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.216 3.040 ... (remaining 74559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.640 Find NCS groups from input model: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.002 0.036 9272 Z= 0.098 Angle : 0.475 6.514 12567 Z= 0.252 Chirality : 0.038 0.127 1433 Planarity : 0.003 0.048 1579 Dihedral : 12.284 88.686 3317 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.56 % Allowed : 8.18 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.38 (0.25), residues: 1143 helix: 1.35 (0.26), residues: 402 sheet: -0.48 (0.32), residues: 277 loop : -1.52 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 208 TYR 0.011 0.001 TYR D 178 PHE 0.008 0.001 PHE B 151 TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9266) covalent geometry : angle 0.47452 (12555) SS BOND : bond 0.00383 ( 6) SS BOND : angle 0.89189 ( 12) hydrogen bonds : bond 0.19656 ( 432) hydrogen bonds : angle 7.00389 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5168 (mttt) REVERT: R 102 TYR cc_start: 0.2572 (OUTLIER) cc_final: 0.1315 (m-10) REVERT: R 127 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.3700 (t80) REVERT: R 134 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.5781 (m-40) REVERT: R 240 PHE cc_start: 0.7442 (m-80) cc_final: 0.7042 (m-80) REVERT: A 51 LYS cc_start: 0.7349 (mttp) cc_final: 0.6886 (pttt) REVERT: A 254 CYS cc_start: 0.5827 (p) cc_final: 0.5391 (p) REVERT: A 318 GLU cc_start: 0.7764 (mt-10) cc_final: 0.6909 (mm-30) REVERT: A 341 ASP cc_start: 0.8317 (t0) cc_final: 0.7732 (m-30) REVERT: B 146 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7497 (mp) REVERT: B 335 PHE cc_start: 0.8734 (m-10) cc_final: 0.8527 (m-80) outliers start: 55 outliers final: 24 residues processed: 247 average time/residue: 0.1020 time to fit residues: 34.6072 Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 134 ASN R 181 GLN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 352 GLN R 373 ASN A 213 HIS A 241 ASN A 269 ASN A 331 ASN A 333 GLN A 347 ASN B 142 HIS D 167 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.207694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.157701 restraints weight = 11465.420| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.42 r_work: 0.3798 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9272 Z= 0.227 Angle : 0.676 11.059 12567 Z= 0.349 Chirality : 0.044 0.180 1433 Planarity : 0.004 0.048 1579 Dihedral : 7.587 57.260 1305 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.25 % Allowed : 13.64 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.55 (0.25), residues: 1143 helix: 1.15 (0.25), residues: 410 sheet: -0.73 (0.32), residues: 270 loop : -1.49 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.020 0.002 TYR D 178 PHE 0.020 0.002 PHE A 336 TRP 0.012 0.002 TRP D 47 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9266) covalent geometry : angle 0.67177 (12555) SS BOND : bond 0.00897 ( 6) SS BOND : angle 2.64856 ( 12) hydrogen bonds : bond 0.04750 ( 432) hydrogen bonds : angle 5.00965 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.5191 (mttt) REVERT: R 102 TYR cc_start: 0.2858 (OUTLIER) cc_final: 0.2003 (t80) REVERT: R 127 TYR cc_start: 0.4415 (OUTLIER) cc_final: 0.3939 (t80) REVERT: R 134 ASN cc_start: 0.7186 (p0) cc_final: 0.5879 (m-40) REVERT: R 240 PHE cc_start: 0.7514 (m-80) cc_final: 0.7283 (m-80) REVERT: R 243 ILE cc_start: 0.7376 (tt) cc_final: 0.7115 (tt) REVERT: A 51 LYS cc_start: 0.7610 (mttp) cc_final: 0.7248 (tptp) REVERT: A 241 ASN cc_start: 0.0756 (OUTLIER) cc_final: 0.0395 (p0) REVERT: A 242 ARG cc_start: 0.5235 (mtp85) cc_final: 0.4665 (mtp180) REVERT: A 254 CYS cc_start: 0.5439 (p) cc_final: 0.5149 (p) REVERT: A 318 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7069 (mm-30) REVERT: A 341 ASP cc_start: 0.8510 (t0) cc_final: 0.8019 (m-30) REVERT: B 163 ASP cc_start: 0.7930 (t70) cc_final: 0.7555 (t0) REVERT: B 258 ASP cc_start: 0.8715 (t0) cc_final: 0.8395 (t0) REVERT: B 325 MET cc_start: 0.7777 (tpp) cc_final: 0.7508 (mpp) REVERT: D 148 ARG cc_start: 0.7982 (mtm-85) cc_final: 0.7569 (mtm110) outliers start: 52 outliers final: 39 residues processed: 216 average time/residue: 0.1027 time to fit residues: 30.5536 Evaluate side-chains 192 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain L residue 1 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.0170 chunk 2 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 47 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.212026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.163661 restraints weight = 11319.653| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.40 r_work: 0.3860 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9272 Z= 0.120 Angle : 0.581 10.268 12567 Z= 0.299 Chirality : 0.041 0.185 1433 Planarity : 0.004 0.045 1579 Dihedral : 7.214 57.906 1294 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.24 % Allowed : 16.46 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.47 (0.25), residues: 1143 helix: 1.28 (0.25), residues: 410 sheet: -0.74 (0.32), residues: 263 loop : -1.46 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.014 0.001 TYR D 178 PHE 0.015 0.001 PHE R 280 TRP 0.020 0.001 TRP R 206 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9266) covalent geometry : angle 0.57672 (12555) SS BOND : bond 0.00602 ( 6) SS BOND : angle 2.43516 ( 12) hydrogen bonds : bond 0.03901 ( 432) hydrogen bonds : angle 4.68561 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5393 (mttt) REVERT: R 102 TYR cc_start: 0.2791 (OUTLIER) cc_final: 0.1934 (t80) REVERT: R 127 TYR cc_start: 0.4145 (OUTLIER) cc_final: 0.3721 (t80) REVERT: R 134 ASN cc_start: 0.7354 (p0) cc_final: 0.5978 (m-40) REVERT: R 243 ILE cc_start: 0.7079 (tt) cc_final: 0.6411 (tt) REVERT: R 266 MET cc_start: 0.5249 (mmp) cc_final: 0.5035 (mmm) REVERT: R 374 MET cc_start: 0.6638 (mmp) cc_final: 0.6410 (mmp) REVERT: A 51 LYS cc_start: 0.7445 (mttp) cc_final: 0.7152 (tptp) REVERT: A 254 CYS cc_start: 0.5609 (p) cc_final: 0.5272 (p) REVERT: A 318 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7067 (mm-30) REVERT: A 341 ASP cc_start: 0.8398 (t0) cc_final: 0.7942 (m-30) REVERT: B 163 ASP cc_start: 0.7642 (t70) cc_final: 0.7255 (t0) REVERT: B 258 ASP cc_start: 0.8486 (t0) cc_final: 0.8147 (t0) REVERT: D 232 LYS cc_start: 0.8386 (tttm) cc_final: 0.8168 (tttm) outliers start: 42 outliers final: 33 residues processed: 205 average time/residue: 0.1014 time to fit residues: 28.6678 Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 333 GLN D 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.208919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158679 restraints weight = 11556.863| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.36 r_work: 0.3838 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9272 Z= 0.184 Angle : 0.648 9.848 12567 Z= 0.328 Chirality : 0.044 0.302 1433 Planarity : 0.004 0.049 1579 Dihedral : 7.304 58.771 1293 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.06 % Allowed : 16.16 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.49 (0.25), residues: 1143 helix: 1.26 (0.25), residues: 410 sheet: -0.74 (0.31), residues: 271 loop : -1.50 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.017 0.001 TYR D 178 PHE 0.010 0.001 PHE D 27 TRP 0.008 0.001 TRP D 47 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9266) covalent geometry : angle 0.64292 (12555) SS BOND : bond 0.00885 ( 6) SS BOND : angle 2.66524 ( 12) hydrogen bonds : bond 0.03961 ( 432) hydrogen bonds : angle 4.63258 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 164 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5298 (mttt) REVERT: R 102 TYR cc_start: 0.2827 (OUTLIER) cc_final: 0.1913 (t80) REVERT: R 127 TYR cc_start: 0.4093 (OUTLIER) cc_final: 0.3732 (t80) REVERT: R 134 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.5987 (m-40) REVERT: R 266 MET cc_start: 0.5455 (mmp) cc_final: 0.5252 (mmm) REVERT: R 374 MET cc_start: 0.6728 (mmp) cc_final: 0.6487 (mmp) REVERT: L 4 SER cc_start: 0.8466 (m) cc_final: 0.8236 (p) REVERT: L 7 MET cc_start: 0.7125 (mmm) cc_final: 0.6851 (mmm) REVERT: A 51 LYS cc_start: 0.7549 (mttp) cc_final: 0.7217 (tptp) REVERT: A 318 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7055 (mm-30) REVERT: A 341 ASP cc_start: 0.8476 (t0) cc_final: 0.7991 (m-30) REVERT: B 101 MET cc_start: 0.8266 (mmm) cc_final: 0.7964 (mtp) REVERT: B 163 ASP cc_start: 0.7669 (t70) cc_final: 0.7304 (t0) REVERT: B 169 TRP cc_start: 0.8399 (m100) cc_final: 0.7929 (m100) REVERT: B 258 ASP cc_start: 0.8441 (t0) cc_final: 0.8155 (t0) REVERT: D 180 MET cc_start: 0.7961 (ptt) cc_final: 0.7728 (ptt) outliers start: 60 outliers final: 46 residues processed: 208 average time/residue: 0.0950 time to fit residues: 27.0301 Evaluate side-chains 201 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 377 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 64 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.205293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.158451 restraints weight = 11427.445| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.31 r_work: 0.3805 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9272 Z= 0.226 Angle : 0.667 9.339 12567 Z= 0.340 Chirality : 0.044 0.212 1433 Planarity : 0.004 0.051 1579 Dihedral : 7.434 58.993 1293 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 6.36 % Allowed : 17.27 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.63 (0.25), residues: 1143 helix: 1.15 (0.25), residues: 411 sheet: -0.90 (0.30), residues: 282 loop : -1.52 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 32 TYR 0.017 0.002 TYR B 145 PHE 0.012 0.002 PHE D 27 TRP 0.009 0.002 TRP B 99 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 9266) covalent geometry : angle 0.66457 (12555) SS BOND : bond 0.01100 ( 6) SS BOND : angle 2.07396 ( 12) hydrogen bonds : bond 0.04056 ( 432) hydrogen bonds : angle 4.67962 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5341 (mttt) REVERT: R 102 TYR cc_start: 0.2846 (OUTLIER) cc_final: 0.1921 (t80) REVERT: R 127 TYR cc_start: 0.4015 (OUTLIER) cc_final: 0.3689 (t80) REVERT: R 134 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.6029 (m-40) REVERT: R 266 MET cc_start: 0.5597 (mmp) cc_final: 0.5359 (mmm) REVERT: A 51 LYS cc_start: 0.7716 (mttp) cc_final: 0.7279 (tptp) REVERT: A 268 LEU cc_start: 0.7160 (mm) cc_final: 0.6851 (mp) REVERT: A 318 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7021 (mm-30) REVERT: A 341 ASP cc_start: 0.8500 (t0) cc_final: 0.7985 (m-30) REVERT: B 163 ASP cc_start: 0.7709 (t70) cc_final: 0.7325 (t0) REVERT: B 169 TRP cc_start: 0.8421 (m100) cc_final: 0.7970 (m100) REVERT: B 258 ASP cc_start: 0.8543 (t0) cc_final: 0.8322 (t0) REVERT: D 206 ARG cc_start: 0.7758 (ptp90) cc_final: 0.7529 (ptt90) outliers start: 63 outliers final: 51 residues processed: 201 average time/residue: 0.0945 time to fit residues: 26.3959 Evaluate side-chains 200 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 145 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 283 CYS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 367 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 109 optimal weight: 0.0270 chunk 5 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 97 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 92 optimal weight: 2.9990 overall best weight: 0.2372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN D 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.212431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.168614 restraints weight = 11360.921| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.26 r_work: 0.3902 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9272 Z= 0.111 Angle : 0.575 9.086 12567 Z= 0.294 Chirality : 0.042 0.213 1433 Planarity : 0.004 0.046 1579 Dihedral : 7.010 59.690 1293 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.15 % Allowed : 18.48 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.32 (0.25), residues: 1143 helix: 1.44 (0.25), residues: 411 sheet: -0.63 (0.32), residues: 268 loop : -1.46 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 148 TYR 0.016 0.001 TYR D 178 PHE 0.009 0.001 PHE A 250 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS L 16 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9266) covalent geometry : angle 0.57374 (12555) SS BOND : bond 0.00595 ( 6) SS BOND : angle 1.26761 ( 12) hydrogen bonds : bond 0.03413 ( 432) hydrogen bonds : angle 4.45321 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5354 (tttt) REVERT: R 102 TYR cc_start: 0.2696 (OUTLIER) cc_final: 0.1822 (t80) REVERT: R 127 TYR cc_start: 0.4270 (OUTLIER) cc_final: 0.4022 (t80) REVERT: R 134 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.5729 (m-40) REVERT: R 266 MET cc_start: 0.5377 (mmp) cc_final: 0.5156 (mmm) REVERT: A 51 LYS cc_start: 0.7709 (mttp) cc_final: 0.7261 (tptp) REVERT: A 254 CYS cc_start: 0.5692 (p) cc_final: 0.5352 (p) REVERT: A 318 GLU cc_start: 0.7811 (mt-10) cc_final: 0.6990 (mm-30) REVERT: A 341 ASP cc_start: 0.8497 (t0) cc_final: 0.8028 (m-30) REVERT: B 163 ASP cc_start: 0.7648 (t70) cc_final: 0.7322 (t0) REVERT: B 171 ILE cc_start: 0.8596 (mm) cc_final: 0.8094 (mm) REVERT: B 258 ASP cc_start: 0.8404 (t0) cc_final: 0.8113 (t0) REVERT: C 29 LYS cc_start: 0.7714 (tppp) cc_final: 0.7473 (tppt) REVERT: D 13 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8795 (mm-40) outliers start: 51 outliers final: 37 residues processed: 208 average time/residue: 0.0898 time to fit residues: 26.3136 Evaluate side-chains 193 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.209065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165445 restraints weight = 11408.493| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.23 r_work: 0.3876 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9272 Z= 0.152 Angle : 0.627 10.287 12567 Z= 0.318 Chirality : 0.042 0.194 1433 Planarity : 0.004 0.046 1579 Dihedral : 6.965 59.136 1290 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.35 % Allowed : 18.89 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.39 (0.25), residues: 1143 helix: 1.37 (0.25), residues: 411 sheet: -0.70 (0.31), residues: 271 loop : -1.45 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 148 TYR 0.017 0.001 TYR D 178 PHE 0.029 0.001 PHE A 336 TRP 0.033 0.002 TRP B 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9266) covalent geometry : angle 0.62600 (12555) SS BOND : bond 0.00791 ( 6) SS BOND : angle 1.30102 ( 12) hydrogen bonds : bond 0.03522 ( 432) hydrogen bonds : angle 4.47222 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5357 (tttt) REVERT: R 102 TYR cc_start: 0.2948 (OUTLIER) cc_final: 0.2044 (t80) REVERT: R 127 TYR cc_start: 0.4385 (OUTLIER) cc_final: 0.4076 (t80) REVERT: R 134 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.5716 (m-40) REVERT: R 266 MET cc_start: 0.5513 (mmp) cc_final: 0.5241 (mmm) REVERT: R 279 SER cc_start: 0.8396 (t) cc_final: 0.7941 (m) REVERT: A 51 LYS cc_start: 0.7771 (mttp) cc_final: 0.7281 (tptp) REVERT: A 186 GLU cc_start: 0.7559 (tt0) cc_final: 0.7203 (tt0) REVERT: A 254 CYS cc_start: 0.6006 (p) cc_final: 0.5572 (p) REVERT: A 318 GLU cc_start: 0.7775 (mt-10) cc_final: 0.6943 (mm-30) REVERT: A 341 ASP cc_start: 0.8491 (t0) cc_final: 0.8031 (m-30) REVERT: B 163 ASP cc_start: 0.7658 (t70) cc_final: 0.7358 (t0) REVERT: B 169 TRP cc_start: 0.8405 (m100) cc_final: 0.7911 (m100) REVERT: B 188 MET cc_start: 0.6892 (mtt) cc_final: 0.6671 (mtm) REVERT: B 258 ASP cc_start: 0.8528 (t0) cc_final: 0.8288 (t0) REVERT: C 29 LYS cc_start: 0.7748 (tppp) cc_final: 0.7495 (tppt) REVERT: D 82 GLN cc_start: 0.7149 (pm20) cc_final: 0.6798 (pm20) REVERT: D 180 MET cc_start: 0.7288 (ptt) cc_final: 0.6996 (ptt) outliers start: 53 outliers final: 42 residues processed: 194 average time/residue: 0.0937 time to fit residues: 25.6460 Evaluate side-chains 191 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 109 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.209414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161070 restraints weight = 11379.134| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.34 r_work: 0.3858 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9272 Z= 0.148 Angle : 0.627 9.478 12567 Z= 0.317 Chirality : 0.043 0.195 1433 Planarity : 0.004 0.047 1579 Dihedral : 6.940 58.880 1290 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.35 % Allowed : 18.69 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.40 (0.25), residues: 1143 helix: 1.36 (0.25), residues: 411 sheet: -0.68 (0.31), residues: 276 loop : -1.48 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 148 TYR 0.014 0.001 TYR D 178 PHE 0.031 0.001 PHE A 336 TRP 0.022 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9266) covalent geometry : angle 0.62618 (12555) SS BOND : bond 0.00793 ( 6) SS BOND : angle 1.17147 ( 12) hydrogen bonds : bond 0.03489 ( 432) hydrogen bonds : angle 4.45547 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5353 (tttt) REVERT: R 102 TYR cc_start: 0.2947 (OUTLIER) cc_final: 0.2035 (t80) REVERT: R 127 TYR cc_start: 0.4377 (OUTLIER) cc_final: 0.4091 (t80) REVERT: R 134 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.5679 (m-40) REVERT: R 266 MET cc_start: 0.5492 (mmp) cc_final: 0.5227 (mmm) REVERT: R 279 SER cc_start: 0.8418 (t) cc_final: 0.7958 (m) REVERT: A 51 LYS cc_start: 0.7783 (mttp) cc_final: 0.7272 (tptp) REVERT: A 186 GLU cc_start: 0.7589 (tt0) cc_final: 0.7294 (tt0) REVERT: A 254 CYS cc_start: 0.5634 (p) cc_final: 0.5303 (p) REVERT: A 318 GLU cc_start: 0.7797 (mt-10) cc_final: 0.6955 (mm-30) REVERT: A 341 ASP cc_start: 0.8487 (t0) cc_final: 0.8006 (m-30) REVERT: B 101 MET cc_start: 0.8165 (mmm) cc_final: 0.7895 (mtp) REVERT: B 163 ASP cc_start: 0.7706 (t70) cc_final: 0.7454 (t0) REVERT: B 169 TRP cc_start: 0.8436 (m100) cc_final: 0.7933 (m100) REVERT: B 188 MET cc_start: 0.6926 (mtt) cc_final: 0.6704 (mtm) REVERT: D 180 MET cc_start: 0.7355 (ptt) cc_final: 0.7148 (ptt) outliers start: 53 outliers final: 45 residues processed: 195 average time/residue: 0.0911 time to fit residues: 25.1171 Evaluate side-chains 199 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 134 ASN Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 56 optimal weight: 0.0970 chunk 27 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.207099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.155696 restraints weight = 11631.685| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.78 r_work: 0.3821 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9272 Z= 0.141 Angle : 0.636 9.138 12567 Z= 0.323 Chirality : 0.043 0.200 1433 Planarity : 0.004 0.047 1579 Dihedral : 6.905 58.321 1290 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.45 % Allowed : 18.59 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.36 (0.25), residues: 1143 helix: 1.38 (0.25), residues: 411 sheet: -0.64 (0.31), residues: 276 loop : -1.46 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 148 TYR 0.014 0.001 TYR D 178 PHE 0.011 0.001 PHE R 278 TRP 0.020 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9266) covalent geometry : angle 0.63547 (12555) SS BOND : bond 0.00755 ( 6) SS BOND : angle 1.14473 ( 12) hydrogen bonds : bond 0.03428 ( 432) hydrogen bonds : angle 4.44041 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 153 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5442 (mttt) REVERT: R 102 TYR cc_start: 0.3003 (OUTLIER) cc_final: 0.2140 (t80) REVERT: R 266 MET cc_start: 0.5312 (mmp) cc_final: 0.5060 (mmm) REVERT: R 278 PHE cc_start: 0.7713 (t80) cc_final: 0.7461 (t80) REVERT: R 279 SER cc_start: 0.8353 (t) cc_final: 0.7880 (m) REVERT: A 51 LYS cc_start: 0.7756 (mttp) cc_final: 0.7226 (tptp) REVERT: A 186 GLU cc_start: 0.7690 (tt0) cc_final: 0.7379 (tt0) REVERT: A 254 CYS cc_start: 0.5542 (p) cc_final: 0.5256 (p) REVERT: A 268 LEU cc_start: 0.6822 (mm) cc_final: 0.6542 (mp) REVERT: A 318 GLU cc_start: 0.7838 (mt-10) cc_final: 0.6765 (mm-30) REVERT: A 341 ASP cc_start: 0.8312 (t0) cc_final: 0.7920 (m-30) REVERT: B 15 LYS cc_start: 0.7775 (tmtt) cc_final: 0.7193 (mtmt) REVERT: B 101 MET cc_start: 0.8250 (mmm) cc_final: 0.8008 (mtp) REVERT: B 163 ASP cc_start: 0.7681 (t70) cc_final: 0.7399 (t0) REVERT: B 169 TRP cc_start: 0.8608 (m100) cc_final: 0.8070 (m100) REVERT: B 171 ILE cc_start: 0.8606 (mm) cc_final: 0.8016 (mm) REVERT: B 188 MET cc_start: 0.6939 (mtt) cc_final: 0.6731 (mtm) REVERT: B 258 ASP cc_start: 0.8506 (t0) cc_final: 0.8286 (t0) REVERT: C 29 LYS cc_start: 0.7299 (tppt) cc_final: 0.6773 (tppt) REVERT: D 82 GLN cc_start: 0.7374 (pm20) cc_final: 0.7079 (pm20) outliers start: 54 outliers final: 47 residues processed: 195 average time/residue: 0.0990 time to fit residues: 26.9881 Evaluate side-chains 199 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 333 GLN Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 102 optimal weight: 0.0370 chunk 13 optimal weight: 0.3980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.208023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.159151 restraints weight = 11582.754| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.61 r_work: 0.3858 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9272 Z= 0.124 Angle : 0.637 10.433 12567 Z= 0.323 Chirality : 0.043 0.206 1433 Planarity : 0.004 0.046 1579 Dihedral : 6.741 57.908 1288 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.75 % Allowed : 18.99 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.28 (0.25), residues: 1143 helix: 1.44 (0.25), residues: 405 sheet: -0.55 (0.31), residues: 271 loop : -1.40 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 148 TYR 0.015 0.001 TYR D 178 PHE 0.011 0.001 PHE R 278 TRP 0.019 0.001 TRP B 211 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9266) covalent geometry : angle 0.63584 (12555) SS BOND : bond 0.00655 ( 6) SS BOND : angle 1.16061 ( 12) hydrogen bonds : bond 0.03334 ( 432) hydrogen bonds : angle 4.43013 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5649 (mttt) REVERT: R 102 TYR cc_start: 0.2875 (OUTLIER) cc_final: 0.2077 (t80) REVERT: R 266 MET cc_start: 0.5386 (mmp) cc_final: 0.4974 (mmm) REVERT: R 278 PHE cc_start: 0.7665 (t80) cc_final: 0.7422 (t80) REVERT: R 279 SER cc_start: 0.8365 (t) cc_final: 0.7907 (m) REVERT: A 51 LYS cc_start: 0.7781 (mttp) cc_final: 0.7235 (tptp) REVERT: A 186 GLU cc_start: 0.7603 (tt0) cc_final: 0.7287 (tt0) REVERT: A 254 CYS cc_start: 0.5475 (p) cc_final: 0.5182 (p) REVERT: A 318 GLU cc_start: 0.7842 (mt-10) cc_final: 0.6780 (mm-30) REVERT: A 341 ASP cc_start: 0.8244 (t0) cc_final: 0.7917 (m-30) REVERT: B 15 LYS cc_start: 0.7759 (tmtt) cc_final: 0.7179 (mtmt) REVERT: B 101 MET cc_start: 0.8254 (mmm) cc_final: 0.8038 (mtp) REVERT: B 138 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7608 (mt-10) REVERT: B 163 ASP cc_start: 0.7616 (t70) cc_final: 0.7365 (t0) REVERT: B 169 TRP cc_start: 0.8562 (m100) cc_final: 0.8034 (m100) REVERT: B 171 ILE cc_start: 0.8575 (mm) cc_final: 0.7989 (mm) REVERT: B 290 ASP cc_start: 0.6884 (m-30) cc_final: 0.6341 (m-30) REVERT: B 325 MET cc_start: 0.7717 (tpp) cc_final: 0.7310 (mmt) REVERT: C 29 LYS cc_start: 0.7306 (tppt) cc_final: 0.6782 (tppt) outliers start: 47 outliers final: 42 residues processed: 196 average time/residue: 0.1000 time to fit residues: 27.2936 Evaluate side-chains 195 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 LYS Chi-restraints excluded: chain R residue 102 TYR Chi-restraints excluded: chain R residue 126 ILE Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 364 LEU Chi-restraints excluded: chain R residue 381 ILE Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 267 GLN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN A 347 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.206809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.157705 restraints weight = 11431.669| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.53 r_work: 0.3843 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9272 Z= 0.146 Angle : 0.656 10.907 12567 Z= 0.334 Chirality : 0.044 0.225 1433 Planarity : 0.004 0.047 1579 Dihedral : 6.756 57.603 1288 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.85 % Allowed : 19.60 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 aren not related in a simple way. whole: -0.32 (0.25), residues: 1143 helix: 1.44 (0.25), residues: 405 sheet: -0.60 (0.31), residues: 273 loop : -1.44 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 148 TYR 0.015 0.001 TYR D 178 PHE 0.011 0.001 PHE R 278 TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9266) covalent geometry : angle 0.65554 (12555) SS BOND : bond 0.00760 ( 6) SS BOND : angle 1.17679 ( 12) hydrogen bonds : bond 0.03469 ( 432) hydrogen bonds : angle 4.46794 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.89 seconds wall clock time: 47 minutes 42.55 seconds (2862.55 seconds total)