Starting phenix.real_space_refine on Thu Mar 13 16:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwp_38740/03_2025/8xwp_38740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwp_38740/03_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_38740/03_2025/8xwp_38740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwp_38740/03_2025/8xwp_38740.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwp_38740/03_2025/8xwp_38740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwp_38740/03_2025/8xwp_38740.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.35, per 1000 atoms: 0.59 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.99 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: 2.63 Time building geometry restraints manager: 2.90 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: 0.650 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.930 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- 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 9266 Z= 0.138 Angle : 0.475 6.514 12555 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 : 8.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP B 99 HIS 0.003 0.001 HIS D 35 PHE 0.008 0.001 PHE B 151 TYR 0.011 0.001 TYR D 178 ARG 0.002 0.000 ARG R 208 *********************** 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 : 0.993 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: 0.2249 time to fit residues: 75.6953 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 : 1.006 ------------------------------------------------------------------------------- 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 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.210694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163046 restraints weight = 11381.028| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.41 r_work: 0.3819 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9266 Z= 0.241 Angle : 0.627 11.416 12555 Z= 0.324 Chirality : 0.043 0.188 1433 Planarity : 0.004 0.047 1579 Dihedral : 7.351 57.480 1305 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.05 % Allowed : 13.33 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1143 helix: 1.27 (0.25), residues: 410 sheet: -0.52 (0.32), residues: 262 loop : -1.50 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.001 PHE A 336 TYR 0.019 0.001 TYR D 178 ARG 0.004 0.000 ARG A 32 *********************** 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: 50 poor density : 175 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5752 (OUTLIER) cc_final: 0.5184 (mttt) REVERT: R 102 TYR cc_start: 0.2774 (OUTLIER) cc_final: 0.1951 (t80) REVERT: R 127 TYR cc_start: 0.4400 (OUTLIER) cc_final: 0.3916 (t80) REVERT: R 134 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.5953 (m-40) REVERT: R 240 PHE cc_start: 0.7448 (m-80) cc_final: 0.7224 (m-80) REVERT: R 243 ILE cc_start: 0.7324 (tt) cc_final: 0.6928 (tt) REVERT: A 51 LYS cc_start: 0.7666 (mttp) cc_final: 0.7271 (tptp) REVERT: A 241 ASN cc_start: 0.0633 (OUTLIER) cc_final: 0.0301 (p0) REVERT: A 254 CYS cc_start: 0.5552 (p) cc_final: 0.5256 (p) REVERT: A 318 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7085 (mm-30) REVERT: A 341 ASP cc_start: 0.8415 (t0) cc_final: 0.7932 (m-30) REVERT: B 163 ASP cc_start: 0.7834 (t70) cc_final: 0.7401 (t0) REVERT: B 258 ASP cc_start: 0.8642 (t0) cc_final: 0.8323 (t0) REVERT: D 148 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7587 (mtm110) REVERT: D 180 MET cc_start: 0.8059 (ptt) cc_final: 0.7858 (ptt) outliers start: 50 outliers final: 33 residues processed: 216 average time/residue: 0.2100 time to fit residues: 63.1442 Evaluate side-chains 189 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 258 HIS Chi-restraints excluded: chain R residue 294 THR Chi-restraints excluded: chain R residue 334 LEU Chi-restraints excluded: chain R residue 358 CYS Chi-restraints excluded: chain R residue 381 ILE 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 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 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 73 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN R 134 ASN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.204015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153761 restraints weight = 11545.707| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.35 r_work: 0.3788 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9266 Z= 0.427 Angle : 0.701 11.483 12555 Z= 0.359 Chirality : 0.045 0.168 1433 Planarity : 0.004 0.048 1579 Dihedral : 7.681 59.497 1296 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.66 % Allowed : 15.45 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1143 helix: 0.98 (0.25), residues: 411 sheet: -0.90 (0.30), residues: 280 loop : -1.60 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 206 HIS 0.008 0.002 HIS B 225 PHE 0.018 0.002 PHE A 336 TYR 0.019 0.002 TYR D 178 ARG 0.007 0.001 ARG D 18 *********************** 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 215 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.5226 (mttt) REVERT: R 102 TYR cc_start: 0.2844 (OUTLIER) cc_final: 0.2272 (t80) REVERT: R 127 TYR cc_start: 0.4216 (OUTLIER) cc_final: 0.3720 (t80) REVERT: R 134 ASN cc_start: 0.7493 (p0) cc_final: 0.6087 (m-40) REVERT: R 243 ILE cc_start: 0.7083 (tt) cc_final: 0.6426 (tt) REVERT: R 266 MET cc_start: 0.5514 (mmp) cc_final: 0.5304 (mmm) REVERT: L 7 MET cc_start: 0.7310 (mmm) cc_final: 0.7041 (mmm) REVERT: A 51 LYS cc_start: 0.7521 (mttp) cc_final: 0.7174 (tptp) REVERT: A 254 CYS cc_start: 0.5683 (p) cc_final: 0.5367 (p) REVERT: A 268 LEU cc_start: 0.7037 (mm) cc_final: 0.6754 (mp) REVERT: A 318 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7027 (mm-30) REVERT: A 341 ASP cc_start: 0.8510 (t0) cc_final: 0.8059 (m-30) REVERT: B 163 ASP cc_start: 0.7901 (t70) cc_final: 0.7542 (t0) REVERT: B 169 TRP cc_start: 0.8441 (m100) cc_final: 0.7979 (m100) REVERT: B 258 ASP cc_start: 0.8610 (t0) cc_final: 0.8383 (t0) outliers start: 56 outliers final: 50 residues processed: 202 average time/residue: 0.2322 time to fit residues: 64.2618 Evaluate side-chains 197 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 177 VAL 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 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 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 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 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 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 B residue 300 LEU 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 12 VAL 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 76 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 142 HIS D 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.209647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.160874 restraints weight = 11373.084| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.33 r_work: 0.3838 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9266 Z= 0.214 Angle : 0.596 10.344 12555 Z= 0.308 Chirality : 0.042 0.191 1433 Planarity : 0.004 0.046 1579 Dihedral : 7.438 57.702 1294 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.25 % Allowed : 17.68 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1143 helix: 1.22 (0.25), residues: 410 sheet: -1.01 (0.32), residues: 266 loop : -1.45 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 206 HIS 0.004 0.001 HIS B 91 PHE 0.026 0.001 PHE A 336 TYR 0.016 0.001 TYR D 178 ARG 0.009 0.000 ARG A 24 *********************** 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 221 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5333 (mttt) REVERT: R 102 TYR cc_start: 0.2829 (OUTLIER) cc_final: 0.1924 (t80) REVERT: R 127 TYR cc_start: 0.4224 (OUTLIER) cc_final: 0.3724 (t80) REVERT: R 134 ASN cc_start: 0.7607 (p0) cc_final: 0.5975 (m-40) REVERT: R 266 MET cc_start: 0.5519 (mmp) cc_final: 0.5305 (mmm) REVERT: A 51 LYS cc_start: 0.7480 (mttp) cc_final: 0.7155 (tptp) REVERT: A 53 MET cc_start: 0.6211 (mtm) cc_final: 0.5672 (mpp) REVERT: A 254 CYS cc_start: 0.5734 (p) cc_final: 0.5389 (p) REVERT: A 268 LEU cc_start: 0.6999 (mm) cc_final: 0.6684 (mp) REVERT: A 318 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7060 (mm-30) REVERT: A 341 ASP cc_start: 0.8367 (t0) cc_final: 0.8027 (m-30) REVERT: B 163 ASP cc_start: 0.7723 (t70) cc_final: 0.7322 (t0) REVERT: B 169 TRP cc_start: 0.8385 (m100) cc_final: 0.7956 (m100) REVERT: B 258 ASP cc_start: 0.8466 (t0) cc_final: 0.8124 (t0) REVERT: B 325 MET cc_start: 0.7860 (tpp) cc_final: 0.7385 (mpp) outliers start: 52 outliers final: 41 residues processed: 211 average time/residue: 0.2107 time to fit residues: 61.3154 Evaluate side-chains 193 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 254 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 283 CYS 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 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 B residue 285 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.210001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.162872 restraints weight = 11316.893| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.40 r_work: 0.3861 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9266 Z= 0.209 Angle : 0.592 8.740 12555 Z= 0.305 Chirality : 0.042 0.192 1433 Planarity : 0.004 0.046 1579 Dihedral : 7.283 58.401 1293 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.45 % Allowed : 17.78 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1143 helix: 1.26 (0.25), residues: 411 sheet: -0.94 (0.31), residues: 272 loop : -1.39 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS A 195 PHE 0.025 0.001 PHE A 336 TYR 0.014 0.001 TYR D 178 ARG 0.006 0.000 ARG A 32 *********************** 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 213 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.5365 (mttt) REVERT: R 102 TYR cc_start: 0.2820 (OUTLIER) cc_final: 0.1902 (t80) REVERT: R 127 TYR cc_start: 0.4029 (OUTLIER) cc_final: 0.3635 (t80) REVERT: R 134 ASN cc_start: 0.7547 (p0) cc_final: 0.5776 (m-40) REVERT: R 266 MET cc_start: 0.5499 (mmp) cc_final: 0.5275 (mmm) REVERT: R 374 MET cc_start: 0.6713 (mmp) cc_final: 0.6397 (mmp) REVERT: R 384 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6643 (mp) REVERT: A 51 LYS cc_start: 0.7563 (mttp) cc_final: 0.7211 (tptp) REVERT: A 53 MET cc_start: 0.6140 (mtm) cc_final: 0.5467 (mtm) REVERT: A 318 GLU cc_start: 0.7889 (mt-10) cc_final: 0.6990 (mm-30) REVERT: A 341 ASP cc_start: 0.8282 (t0) cc_final: 0.8026 (m-30) REVERT: B 101 MET cc_start: 0.8179 (mmm) cc_final: 0.7885 (mtp) REVERT: B 163 ASP cc_start: 0.7631 (t70) cc_final: 0.7267 (t0) REVERT: B 169 TRP cc_start: 0.8400 (m100) cc_final: 0.7937 (m100) REVERT: B 258 ASP cc_start: 0.8426 (t0) cc_final: 0.8154 (t0) REVERT: B 325 MET cc_start: 0.7816 (tpp) cc_final: 0.7529 (mpp) outliers start: 54 outliers final: 42 residues processed: 201 average time/residue: 0.2124 time to fit residues: 59.7762 Evaluate side-chains 193 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 R residue 384 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 269 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU 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 83 MET Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 154 LEU 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 90 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 333 GLN D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.203043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152603 restraints weight = 11575.017| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.75 r_work: 0.3775 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9266 Z= 0.295 Angle : 0.636 9.323 12555 Z= 0.327 Chirality : 0.043 0.186 1433 Planarity : 0.004 0.049 1579 Dihedral : 7.369 58.844 1293 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 5.86 % Allowed : 17.37 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1143 helix: 1.21 (0.25), residues: 411 sheet: -1.01 (0.30), residues: 288 loop : -1.43 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP R 226 HIS 0.006 0.001 HIS B 225 PHE 0.024 0.002 PHE A 336 TYR 0.016 0.001 TYR D 178 ARG 0.005 0.000 ARG D 148 *********************** 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 218 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 160 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5293 (mttt) REVERT: R 102 TYR cc_start: 0.2780 (OUTLIER) cc_final: 0.1945 (t80) REVERT: R 127 TYR cc_start: 0.4221 (OUTLIER) cc_final: 0.3981 (t80) REVERT: R 134 ASN cc_start: 0.7585 (p0) cc_final: 0.5857 (m-40) REVERT: R 266 MET cc_start: 0.5325 (mmp) cc_final: 0.4864 (mmm) REVERT: R 279 SER cc_start: 0.8409 (t) cc_final: 0.7958 (m) REVERT: A 51 LYS cc_start: 0.7279 (mttp) cc_final: 0.6901 (tptp) REVERT: A 268 LEU cc_start: 0.6537 (mm) cc_final: 0.6292 (mp) REVERT: A 318 GLU cc_start: 0.7923 (mt-10) cc_final: 0.6833 (mm-30) REVERT: A 341 ASP cc_start: 0.8236 (t0) cc_final: 0.7950 (m-30) REVERT: B 163 ASP cc_start: 0.7716 (t70) cc_final: 0.7297 (t0) REVERT: B 169 TRP cc_start: 0.8566 (m100) cc_final: 0.8076 (m100) REVERT: B 258 ASP cc_start: 0.8577 (t0) cc_final: 0.8340 (t0) REVERT: B 325 MET cc_start: 0.7818 (tpp) cc_final: 0.7460 (mpp) REVERT: C 29 LYS cc_start: 0.7377 (tppt) cc_final: 0.7024 (tppt) REVERT: D 206 ARG cc_start: 0.7848 (ptp90) cc_final: 0.7604 (ptt90) outliers start: 58 outliers final: 46 residues processed: 202 average time/residue: 0.2139 time to fit residues: 59.4719 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 : 1.072 ------------------------------------------------------------------------------- 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 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 381 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 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 269 ILE 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 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 154 LEU Chi-restraints excluded: chain D residue 187 VAL 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 80 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.205046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155045 restraints weight = 11712.644| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.54 r_work: 0.3818 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9266 Z= 0.218 Angle : 0.607 8.762 12555 Z= 0.312 Chirality : 0.042 0.190 1433 Planarity : 0.004 0.048 1579 Dihedral : 7.279 59.211 1293 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.16 % Allowed : 17.68 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1143 helix: 1.25 (0.25), residues: 411 sheet: -0.90 (0.30), residues: 285 loop : -1.42 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 226 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE R 278 TYR 0.014 0.001 TYR D 178 ARG 0.006 0.000 ARG D 148 *********************** 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 224 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5982 (OUTLIER) cc_final: 0.5262 (mttt) REVERT: R 102 TYR cc_start: 0.2778 (OUTLIER) cc_final: 0.1902 (t80) REVERT: R 127 TYR cc_start: 0.4200 (OUTLIER) cc_final: 0.3932 (t80) REVERT: R 134 ASN cc_start: 0.7307 (OUTLIER) cc_final: 0.5796 (m-40) REVERT: R 266 MET cc_start: 0.5215 (mmp) cc_final: 0.4954 (mmm) REVERT: R 279 SER cc_start: 0.8425 (t) cc_final: 0.7968 (m) REVERT: R 374 MET cc_start: 0.6707 (mmp) cc_final: 0.6368 (mmp) REVERT: R 384 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6560 (mp) REVERT: A 51 LYS cc_start: 0.7374 (mttp) cc_final: 0.6968 (tptp) REVERT: A 254 CYS cc_start: 0.5514 (p) cc_final: 0.5214 (p) REVERT: A 268 LEU cc_start: 0.6563 (mm) cc_final: 0.6348 (mp) REVERT: A 318 GLU cc_start: 0.7853 (mt-10) cc_final: 0.6774 (mm-30) REVERT: A 341 ASP cc_start: 0.8234 (t0) cc_final: 0.7972 (m-30) REVERT: B 163 ASP cc_start: 0.7611 (t70) cc_final: 0.7223 (t0) REVERT: B 169 TRP cc_start: 0.8494 (m100) cc_final: 0.7990 (m100) REVERT: B 258 ASP cc_start: 0.8511 (t0) cc_final: 0.8262 (t0) REVERT: B 259 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: B 325 MET cc_start: 0.7773 (tpp) cc_final: 0.7465 (mpp) REVERT: C 29 LYS cc_start: 0.7405 (tppt) cc_final: 0.7018 (tppt) REVERT: C 40 TYR cc_start: 0.8302 (t80) cc_final: 0.8050 (t80) REVERT: D 180 MET cc_start: 0.7883 (ptt) cc_final: 0.7569 (ptt) outliers start: 61 outliers final: 51 residues processed: 209 average time/residue: 0.2071 time to fit residues: 60.0112 Evaluate side-chains 208 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 151 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 174 CYS 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 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 381 ILE Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain A residue 53 MET 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 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 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 308 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 156 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 = 0.4490 r_free = 0.4490 target = 0.203086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.152863 restraints weight = 11767.479| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.55 r_work: 0.3798 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9266 Z= 0.301 Angle : 0.659 10.887 12555 Z= 0.338 Chirality : 0.044 0.187 1433 Planarity : 0.004 0.050 1579 Dihedral : 7.342 59.742 1293 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 6.77 % Allowed : 17.58 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1143 helix: 1.17 (0.25), residues: 411 sheet: -0.81 (0.30), residues: 284 loop : -1.49 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 226 HIS 0.006 0.001 HIS B 225 PHE 0.013 0.002 PHE R 278 TYR 0.016 0.001 TYR D 178 ARG 0.006 0.000 ARG D 148 *********************** 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 222 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 155 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.5883 (OUTLIER) cc_final: 0.5247 (mttt) REVERT: R 102 TYR cc_start: 0.2786 (OUTLIER) cc_final: 0.1921 (t80) REVERT: R 127 TYR cc_start: 0.4147 (OUTLIER) cc_final: 0.3911 (t80) REVERT: R 134 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.5842 (m-40) REVERT: R 266 MET cc_start: 0.5236 (mmp) cc_final: 0.4975 (mmm) REVERT: R 279 SER cc_start: 0.8382 (t) cc_final: 0.7927 (m) REVERT: R 374 MET cc_start: 0.6717 (mmp) cc_final: 0.6380 (mmp) REVERT: R 384 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6552 (mp) REVERT: A 51 LYS cc_start: 0.7340 (mttp) cc_final: 0.6914 (tptp) REVERT: A 254 CYS cc_start: 0.5557 (p) cc_final: 0.5245 (p) REVERT: A 268 LEU cc_start: 0.6614 (mm) cc_final: 0.6393 (mp) REVERT: A 318 GLU cc_start: 0.7786 (mt-10) cc_final: 0.6788 (mm-30) REVERT: A 341 ASP cc_start: 0.8260 (t0) cc_final: 0.7946 (m-30) REVERT: B 163 ASP cc_start: 0.7639 (t70) cc_final: 0.7267 (t0) REVERT: B 169 TRP cc_start: 0.8538 (m100) cc_final: 0.8024 (m100) REVERT: B 171 ILE cc_start: 0.8716 (mm) cc_final: 0.8487 (mt) REVERT: B 258 ASP cc_start: 0.8543 (t0) cc_final: 0.8299 (t0) REVERT: B 259 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: B 325 MET cc_start: 0.7790 (tpp) cc_final: 0.7457 (mpp) REVERT: C 29 LYS cc_start: 0.7510 (tppt) cc_final: 0.7140 (tppt) REVERT: D 180 MET cc_start: 0.7911 (ptt) cc_final: 0.7619 (ptt) outliers start: 67 outliers final: 56 residues processed: 205 average time/residue: 0.2048 time to fit residues: 58.5886 Evaluate side-chains 207 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 145 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain R residue 224 LEU 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 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 381 ILE Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain A residue 182 THR 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 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 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 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 308 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 101 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 267 GLN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 351 ASN A 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.202709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151940 restraints weight = 11483.662| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.65 r_work: 0.3795 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9266 Z= 0.281 Angle : 0.658 10.475 12555 Z= 0.336 Chirality : 0.044 0.206 1433 Planarity : 0.004 0.049 1579 Dihedral : 7.362 59.937 1293 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.77 % Allowed : 17.78 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1143 helix: 1.06 (0.25), residues: 411 sheet: -0.99 (0.30), residues: 294 loop : -1.41 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 226 HIS 0.005 0.001 HIS B 225 PHE 0.014 0.001 PHE A 199 TYR 0.016 0.001 TYR D 178 ARG 0.007 0.000 ARG D 148 *********************** 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 218 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 151 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6006 (OUTLIER) cc_final: 0.5308 (mttt) REVERT: R 102 TYR cc_start: 0.2779 (OUTLIER) cc_final: 0.2089 (t80) REVERT: R 127 TYR cc_start: 0.4165 (OUTLIER) cc_final: 0.3941 (t80) REVERT: R 134 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.5971 (m-40) REVERT: R 266 MET cc_start: 0.5210 (mmp) cc_final: 0.4953 (mmm) REVERT: R 279 SER cc_start: 0.8427 (t) cc_final: 0.7980 (m) REVERT: R 374 MET cc_start: 0.6692 (mmp) cc_final: 0.6355 (mmp) REVERT: R 384 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6484 (mp) REVERT: A 51 LYS cc_start: 0.7283 (mttp) cc_final: 0.6849 (tptp) REVERT: A 186 GLU cc_start: 0.7744 (tt0) cc_final: 0.7487 (tt0) REVERT: A 254 CYS cc_start: 0.5566 (p) cc_final: 0.5246 (p) REVERT: A 268 LEU cc_start: 0.6588 (mm) cc_final: 0.6366 (mp) REVERT: A 318 GLU cc_start: 0.7794 (mt-10) cc_final: 0.6794 (mm-30) REVERT: A 341 ASP cc_start: 0.8246 (t0) cc_final: 0.7934 (m-30) REVERT: B 15 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7208 (mtmt) REVERT: B 163 ASP cc_start: 0.7621 (t70) cc_final: 0.7240 (t0) REVERT: B 169 TRP cc_start: 0.8557 (m100) cc_final: 0.8047 (m100) REVERT: B 171 ILE cc_start: 0.8751 (mm) cc_final: 0.8542 (mt) REVERT: B 258 ASP cc_start: 0.8532 (t0) cc_final: 0.8289 (t0) REVERT: B 259 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: B 325 MET cc_start: 0.7802 (tpp) cc_final: 0.7471 (mpp) REVERT: C 29 LYS cc_start: 0.7537 (tppt) cc_final: 0.7190 (tppt) REVERT: D 180 MET cc_start: 0.7898 (ptt) cc_final: 0.7613 (ptt) outliers start: 67 outliers final: 55 residues processed: 202 average time/residue: 0.1965 time to fit residues: 56.0753 Evaluate side-chains 209 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 148 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 209 ILE 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 381 ILE Chi-restraints excluded: chain R residue 384 ILE Chi-restraints excluded: chain A residue 182 THR 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 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 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 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 308 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 chunk 78 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 21 optimal weight: 0.0970 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 351 ASN R 373 ASN A 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.206873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.158432 restraints weight = 11633.226| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.61 r_work: 0.3858 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9266 Z= 0.169 Angle : 0.608 10.400 12555 Z= 0.311 Chirality : 0.043 0.208 1433 Planarity : 0.004 0.046 1579 Dihedral : 7.090 58.967 1293 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.56 % Allowed : 19.09 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1143 helix: 1.29 (0.25), residues: 403 sheet: -0.76 (0.31), residues: 281 loop : -1.34 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.011 0.001 PHE R 278 TYR 0.013 0.001 TYR D 178 ARG 0.007 0.000 ARG D 148 ********************** 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 214 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 159 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 101 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5535 (mttt) REVERT: R 102 TYR cc_start: 0.2647 (OUTLIER) cc_final: 0.1837 (t80) REVERT: R 134 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.5804 (m-40) REVERT: R 169 PHE cc_start: 0.6275 (m-80) cc_final: 0.5791 (m-80) REVERT: R 266 MET cc_start: 0.5214 (mmp) cc_final: 0.4959 (mmm) REVERT: R 279 SER cc_start: 0.8653 (t) cc_final: 0.8218 (m) REVERT: A 51 LYS cc_start: 0.7253 (mttp) cc_final: 0.6816 (tptp) REVERT: A 186 GLU cc_start: 0.7621 (tt0) cc_final: 0.7399 (tt0) REVERT: A 254 CYS cc_start: 0.5468 (p) cc_final: 0.5152 (p) REVERT: A 318 GLU cc_start: 0.7752 (mt-10) cc_final: 0.6771 (mm-30) REVERT: A 341 ASP cc_start: 0.8200 (t0) cc_final: 0.7943 (m-30) REVERT: B 15 LYS cc_start: 0.7695 (tmtt) cc_final: 0.7100 (mtmt) REVERT: B 146 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 163 ASP cc_start: 0.7698 (t70) cc_final: 0.7401 (t0) REVERT: B 169 TRP cc_start: 0.8524 (m100) cc_final: 0.8024 (m100) REVERT: B 171 ILE cc_start: 0.8700 (mm) cc_final: 0.8139 (mm) REVERT: B 258 ASP cc_start: 0.8502 (t0) cc_final: 0.8272 (t0) REVERT: B 259 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: B 325 MET cc_start: 0.7878 (tpp) cc_final: 0.7603 (mpp) REVERT: C 29 LYS cc_start: 0.7439 (tppt) cc_final: 0.6935 (tppt) REVERT: D 180 MET cc_start: 0.7744 (ptt) cc_final: 0.7481 (ptt) outliers start: 55 outliers final: 43 residues processed: 201 average time/residue: 0.2561 time to fit residues: 72.1544 Evaluate side-chains 199 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 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 209 ILE Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 261 GLN Chi-restraints excluded: chain R residue 283 CYS 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 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 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 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS 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 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 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 0.0670 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.208131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.157965 restraints weight = 11568.970| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.72 r_work: 0.3858 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9266 Z= 0.170 Angle : 0.618 10.149 12555 Z= 0.314 Chirality : 0.042 0.218 1433 Planarity : 0.004 0.046 1579 Dihedral : 6.841 58.044 1290 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.85 % Allowed : 20.30 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1143 helix: 1.36 (0.25), residues: 403 sheet: -0.64 (0.32), residues: 276 loop : -1.31 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 332 HIS 0.002 0.001 HIS L 16 PHE 0.013 0.001 PHE A 334 TYR 0.013 0.001 TYR R 281 ARG 0.007 0.000 ARG D 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5343.75 seconds wall clock time: 94 minutes 48.42 seconds (5688.42 seconds total)