Starting phenix.real_space_refine on Sat Aug 23 03:47:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3z_36869/08_2025/8k3z_36869_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3z_36869/08_2025/8k3z_36869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k3z_36869/08_2025/8k3z_36869_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3z_36869/08_2025/8k3z_36869_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3z_36869/08_2025/8k3z_36869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3z_36869/08_2025/8k3z_36869.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.131 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 65 5.16 5 C 6093 2.51 5 N 1622 2.21 5 O 1756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9536 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2390 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 10, 'TRANS': 285} Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2589 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1850 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 230} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 510 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 425 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 1.97, per 1000 atoms: 0.21 Number of scatterers: 9536 At special positions: 0 Unit cell: (158.1, 124.1, 96.9, 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 65 16.00 O 1756 8.00 N 1622 7.00 C 6093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 186 " distance=2.04 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 320.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 31 through 65 removed outlier: 3.650A pdb=" N ILE A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 72 through 90 removed outlier: 5.191A pdb=" N LEU A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.623A pdb=" N TRP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 140 removed outlier: 4.006A pdb=" N LEU A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS A 113 " --> pdb=" O CYS A 109 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.973A pdb=" N VAL A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.764A pdb=" N VAL A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 227 removed outlier: 3.708A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 267 removed outlier: 3.838A pdb=" N ALA A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 273 through 292 removed outlier: 3.561A pdb=" N GLU A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Proline residue: A 299 - end of helix Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'B' and resid 9 through 24 removed outlier: 3.578A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 51 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.475A pdb=" N ILE C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS C 213 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.608A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 4.187A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.816A pdb=" N GLN C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.804A pdb=" N GLN D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.619A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.596A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.688A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.046A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.719A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.923A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.727A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.720A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 191 removed outlier: 6.242A pdb=" N VAL C 34 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE C 199 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 28 through 29 removed outlier: 4.318A pdb=" N GLN D 37 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.011A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.223A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.534A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1543 1.29 - 1.43: 2578 1.43 - 1.56: 5530 1.56 - 1.69: 0 1.69 - 1.83: 90 Bond restraints: 9741 Sorted by residual: bond pdb=" C ILE A 213 " pdb=" O ILE A 213 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.12e-02 7.97e+03 4.96e+01 bond pdb=" C ILE A 213 " pdb=" N VAL A 214 " ideal model delta sigma weight residual 1.334 1.270 0.064 1.25e-02 6.40e+03 2.61e+01 bond pdb=" CA LEU D 26 " pdb=" C LEU D 26 " ideal model delta sigma weight residual 1.520 1.465 0.055 1.12e-02 7.97e+03 2.40e+01 bond pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.23e-02 6.61e+03 1.74e+01 bond pdb=" C GLY A 212 " pdb=" N ILE A 213 " ideal model delta sigma weight residual 1.334 1.296 0.038 1.26e-02 6.30e+03 8.89e+00 ... (remaining 9736 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 13057 2.50 - 5.00: 118 5.00 - 7.50: 16 7.50 - 10.01: 2 10.01 - 12.51: 1 Bond angle restraints: 13194 Sorted by residual: angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 110.53 117.67 -7.14 9.40e-01 1.13e+00 5.77e+01 angle pdb=" C ILE A 213 " pdb=" CA ILE A 213 " pdb=" CB ILE A 213 " ideal model delta sigma weight residual 112.02 102.48 9.54 1.31e+00 5.83e-01 5.30e+01 angle pdb=" CA GLY A 212 " pdb=" C GLY A 212 " pdb=" N ILE A 213 " ideal model delta sigma weight residual 117.04 122.26 -5.22 9.90e-01 1.02e+00 2.78e+01 angle pdb=" O GLY A 212 " pdb=" C GLY A 212 " pdb=" N ILE A 213 " ideal model delta sigma weight residual 122.19 117.13 5.06 9.60e-01 1.09e+00 2.78e+01 angle pdb=" C ALA D 35 " pdb=" CA ALA D 35 " pdb=" CB ALA D 35 " ideal model delta sigma weight residual 116.54 110.67 5.87 1.15e+00 7.56e-01 2.60e+01 ... (remaining 13189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4951 17.65 - 35.30: 610 35.30 - 52.95: 190 52.95 - 70.60: 36 70.60 - 88.26: 6 Dihedral angle restraints: 5793 sinusoidal: 2257 harmonic: 3536 Sorted by residual: dihedral pdb=" CA LEU D 55 " pdb=" C LEU D 55 " pdb=" N LYS D 56 " pdb=" CA LYS D 56 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASP A 74 " pdb=" C ASP A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 5790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1102 0.044 - 0.088: 297 0.088 - 0.131: 90 0.131 - 0.175: 4 0.175 - 0.219: 2 Chirality restraints: 1495 Sorted by residual: chirality pdb=" CG LEU D 26 " pdb=" CB LEU D 26 " pdb=" CD1 LEU D 26 " pdb=" CD2 LEU D 26 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1492 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 111 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.18e+00 pdb=" C ALA A 111 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA A 111 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 112 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO S 236 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 236 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2592 2.81 - 3.33: 8213 3.33 - 3.85: 15338 3.85 - 4.38: 18816 4.38 - 4.90: 32240 Nonbonded interactions: 77199 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" NH1 ARG A 77 " model vdw 2.284 3.120 nonbonded pdb=" N ASP B 333 " pdb=" OD1 ASP B 333 " model vdw 2.308 3.120 nonbonded pdb=" NZ LYS B 89 " pdb=" OD1 ASP C 20 " model vdw 2.309 3.120 nonbonded pdb=" OG SER A 71 " pdb=" OD1 ASP A 74 " model vdw 2.320 3.040 nonbonded pdb=" OE1 GLN A 66 " pdb=" OG SER A 312 " model vdw 2.330 3.040 ... (remaining 77194 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.003 0.079 9747 Z= 0.183 Angle : 0.625 12.508 13206 Z= 0.373 Chirality : 0.043 0.219 1495 Planarity : 0.004 0.050 1666 Dihedral : 17.241 88.256 3493 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.48 % Allowed : 24.27 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.24), residues: 1199 helix: 1.09 (0.27), residues: 384 sheet: 0.79 (0.30), residues: 298 loop : -1.25 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 242 TYR 0.028 0.001 TYR S 235 PHE 0.012 0.001 PHE B 151 TRP 0.014 0.001 TRP D 57 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9741) covalent geometry : angle 0.62399 (13194) SS BOND : bond 0.00583 ( 6) SS BOND : angle 1.53563 ( 12) hydrogen bonds : bond 0.13973 ( 421) hydrogen bonds : angle 6.04303 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.367 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 215 GLU cc_start: 0.7489 (mp0) cc_final: 0.7193 (mm-30) REVERT: D 31 THR cc_start: 0.4658 (OUTLIER) cc_final: 0.4331 (t) REVERT: G 29 LYS cc_start: 0.8049 (mttp) cc_final: 0.7589 (mmmm) REVERT: S 235 TYR cc_start: 0.7102 (OUTLIER) cc_final: 0.5857 (t80) outliers start: 36 outliers final: 28 residues processed: 139 average time/residue: 0.5280 time to fit residues: 78.4378 Evaluate side-chains 132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 67 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 223 ASP Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN D 33 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.106597 restraints weight = 10654.930| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.57 r_work: 0.2765 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9747 Z= 0.178 Angle : 0.610 8.581 13206 Z= 0.326 Chirality : 0.045 0.275 1495 Planarity : 0.005 0.051 1666 Dihedral : 7.062 55.341 1362 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.32 % Allowed : 20.89 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.24), residues: 1199 helix: 1.36 (0.27), residues: 388 sheet: 0.79 (0.30), residues: 298 loop : -1.19 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.027 0.002 TYR S 235 PHE 0.015 0.002 PHE C 196 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9741) covalent geometry : angle 0.60884 (13194) SS BOND : bond 0.00795 ( 6) SS BOND : angle 1.37715 ( 12) hydrogen bonds : bond 0.05913 ( 421) hydrogen bonds : angle 4.83543 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 107 time to evaluate : 0.332 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7350 (mmm-85) REVERT: A 236 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7064 (mttm) REVERT: B 118 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8062 (p0) REVERT: B 175 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: B 217 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8406 (pmm) REVERT: B 234 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8871 (m-80) REVERT: C 5 LEU cc_start: 0.8332 (mt) cc_final: 0.7996 (mp) REVERT: S 11 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8384 (tt) REVERT: S 235 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.6562 (t80) outliers start: 55 outliers final: 24 residues processed: 151 average time/residue: 0.5536 time to fit residues: 89.0117 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107445 restraints weight = 10678.989| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.38 r_work: 0.2716 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9747 Z= 0.172 Angle : 0.600 8.427 13206 Z= 0.321 Chirality : 0.045 0.282 1495 Planarity : 0.004 0.046 1666 Dihedral : 6.296 56.945 1333 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.22 % Allowed : 21.08 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.24), residues: 1199 helix: 1.41 (0.27), residues: 389 sheet: 0.72 (0.29), residues: 302 loop : -1.25 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 70 TYR 0.027 0.002 TYR S 235 PHE 0.016 0.002 PHE B 151 TRP 0.018 0.002 TRP D 57 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9741) covalent geometry : angle 0.59906 (13194) SS BOND : bond 0.00802 ( 6) SS BOND : angle 1.37386 ( 12) hydrogen bonds : bond 0.05728 ( 421) hydrogen bonds : angle 4.71954 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 0.266 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7355 (mmm-85) REVERT: A 184 TYR cc_start: 0.7937 (m-80) cc_final: 0.7658 (m-10) REVERT: A 226 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 236 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7206 (mttm) REVERT: B 46 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8119 (mtp85) REVERT: B 118 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8062 (p0) REVERT: B 175 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7812 (mp10) REVERT: B 217 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8446 (pmm) REVERT: B 234 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8916 (m-80) REVERT: C 5 LEU cc_start: 0.8431 (mt) cc_final: 0.8067 (mp) REVERT: C 21 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8595 (ttm170) REVERT: C 330 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6964 (mtmt) REVERT: S 11 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8391 (tt) REVERT: S 90 ASP cc_start: 0.9079 (m-30) cc_final: 0.8873 (m-30) REVERT: S 235 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6530 (t80) outliers start: 54 outliers final: 25 residues processed: 154 average time/residue: 0.6054 time to fit residues: 98.6405 Evaluate side-chains 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 97 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 111 optimal weight: 0.0170 chunk 77 optimal weight: 0.4980 chunk 104 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.111288 restraints weight = 10732.547| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.31 r_work: 0.2834 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 9747 Z= 0.103 Angle : 0.513 7.501 13206 Z= 0.277 Chirality : 0.042 0.190 1495 Planarity : 0.004 0.049 1666 Dihedral : 5.376 54.649 1324 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.90 % Allowed : 23.21 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.24), residues: 1199 helix: 1.74 (0.27), residues: 389 sheet: 0.73 (0.29), residues: 303 loop : -1.18 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 70 TYR 0.017 0.001 TYR S 235 PHE 0.012 0.001 PHE C 189 TRP 0.017 0.001 TRP D 57 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9741) covalent geometry : angle 0.51269 (13194) SS BOND : bond 0.00489 ( 6) SS BOND : angle 0.89125 ( 12) hydrogen bonds : bond 0.04102 ( 421) hydrogen bonds : angle 4.39267 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.382 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6430 (mtm180) REVERT: B 46 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8085 (mtp85) REVERT: B 217 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8351 (pmm) REVERT: B 234 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8829 (m-80) REVERT: C 5 LEU cc_start: 0.8374 (mt) cc_final: 0.8030 (mp) REVERT: C 330 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6909 (mtmt) REVERT: S 11 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8379 (tt) REVERT: S 235 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.5541 (t80) outliers start: 30 outliers final: 13 residues processed: 138 average time/residue: 0.6379 time to fit residues: 93.1650 Evaluate side-chains 128 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 57 TRP Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 42 optimal weight: 0.0040 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 17 GLN C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106920 restraints weight = 10769.356| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.23 r_work: 0.2774 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9747 Z= 0.160 Angle : 0.581 8.908 13206 Z= 0.311 Chirality : 0.044 0.258 1495 Planarity : 0.004 0.051 1666 Dihedral : 5.653 58.796 1323 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.45 % Allowed : 22.34 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.24), residues: 1199 helix: 1.55 (0.27), residues: 396 sheet: 0.80 (0.30), residues: 296 loop : -1.31 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 242 TYR 0.024 0.002 TYR S 235 PHE 0.015 0.002 PHE C 196 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9741) covalent geometry : angle 0.57976 (13194) SS BOND : bond 0.00775 ( 6) SS BOND : angle 1.37775 ( 12) hydrogen bonds : bond 0.05424 ( 421) hydrogen bonds : angle 4.58245 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.403 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6499 (mtm180) REVERT: B 46 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8110 (mtp85) REVERT: B 175 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: B 217 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8385 (pmm) REVERT: B 234 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: C 5 LEU cc_start: 0.8429 (mt) cc_final: 0.8033 (mp) REVERT: S 11 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8385 (tt) REVERT: S 235 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6336 (t80) outliers start: 46 outliers final: 20 residues processed: 137 average time/residue: 0.5987 time to fit residues: 87.0157 Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 17 GLN C 188 HIS ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.107944 restraints weight = 10668.933| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.29 r_work: 0.2782 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9747 Z= 0.135 Angle : 0.552 9.892 13206 Z= 0.296 Chirality : 0.043 0.243 1495 Planarity : 0.004 0.045 1666 Dihedral : 5.545 58.092 1323 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.97 % Allowed : 23.02 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.24), residues: 1199 helix: 1.70 (0.27), residues: 390 sheet: 0.83 (0.29), residues: 294 loop : -1.25 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 70 TYR 0.023 0.001 TYR S 235 PHE 0.013 0.001 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9741) covalent geometry : angle 0.55138 (13194) SS BOND : bond 0.00642 ( 6) SS BOND : angle 1.14941 ( 12) hydrogen bonds : bond 0.04957 ( 421) hydrogen bonds : angle 4.51447 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.250 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 22 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6559 (mtm180) REVERT: B 23 LYS cc_start: 0.7607 (tppt) cc_final: 0.7282 (tptm) REVERT: B 46 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8103 (mtp85) REVERT: B 175 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: B 217 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8369 (pmm) REVERT: B 234 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8855 (m-80) REVERT: C 5 LEU cc_start: 0.8416 (mt) cc_final: 0.8035 (mp) REVERT: S 11 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8375 (tt) REVERT: S 235 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.5975 (t80) outliers start: 41 outliers final: 20 residues processed: 143 average time/residue: 0.5746 time to fit residues: 87.2074 Evaluate side-chains 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 17 GLN C 188 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.150327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.107966 restraints weight = 10728.126| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.23 r_work: 0.2790 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9747 Z= 0.128 Angle : 0.546 10.675 13206 Z= 0.292 Chirality : 0.043 0.232 1495 Planarity : 0.004 0.049 1666 Dihedral : 5.483 58.227 1322 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.26 % Allowed : 22.63 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.24), residues: 1199 helix: 1.76 (0.27), residues: 390 sheet: 0.90 (0.29), residues: 292 loop : -1.25 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.021 0.001 TYR S 235 PHE 0.012 0.001 PHE C 189 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9741) covalent geometry : angle 0.54516 (13194) SS BOND : bond 0.00626 ( 6) SS BOND : angle 1.13384 ( 12) hydrogen bonds : bond 0.04814 ( 421) hydrogen bonds : angle 4.48178 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.288 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6595 (mtm180) REVERT: B 23 LYS cc_start: 0.7605 (tppt) cc_final: 0.7289 (tptm) REVERT: B 46 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8107 (mtp85) REVERT: B 118 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8112 (p0) REVERT: B 175 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7934 (mp10) REVERT: B 217 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8364 (pmm) REVERT: B 234 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: C 5 LEU cc_start: 0.8422 (mt) cc_final: 0.8043 (mp) REVERT: C 21 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8513 (ttm110) REVERT: S 11 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8371 (tt) REVERT: S 13 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8094 (tp40) REVERT: S 235 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.5977 (t80) outliers start: 44 outliers final: 19 residues processed: 142 average time/residue: 0.5777 time to fit residues: 87.2070 Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 65 TYR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.0570 chunk 96 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 HIS B 17 GLN C 57 HIS C 188 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111159 restraints weight = 10661.156| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.26 r_work: 0.2820 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9747 Z= 0.107 Angle : 0.525 11.168 13206 Z= 0.281 Chirality : 0.042 0.201 1495 Planarity : 0.004 0.046 1666 Dihedral : 5.066 57.791 1318 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.48 % Allowed : 23.50 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.24), residues: 1199 helix: 1.92 (0.27), residues: 390 sheet: 0.97 (0.29), residues: 291 loop : -1.23 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 20 TYR 0.018 0.001 TYR S 235 PHE 0.014 0.001 PHE C 189 TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 9741) covalent geometry : angle 0.52454 (13194) SS BOND : bond 0.00513 ( 6) SS BOND : angle 0.95434 ( 12) hydrogen bonds : bond 0.04305 ( 421) hydrogen bonds : angle 4.38408 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.265 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6642 (tm) REVERT: B 22 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6603 (mtm180) REVERT: B 23 LYS cc_start: 0.7555 (tppt) cc_final: 0.7235 (tptm) REVERT: B 46 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8105 (mtp85) REVERT: B 175 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: B 215 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7531 (mp0) REVERT: B 217 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8359 (pmm) REVERT: B 234 PHE cc_start: 0.9204 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: C 5 LEU cc_start: 0.8445 (mt) cc_final: 0.8083 (mp) REVERT: C 21 ARG cc_start: 0.8757 (ttm110) cc_final: 0.8545 (ttm110) REVERT: S 11 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8379 (tt) REVERT: S 235 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.5515 (t80) outliers start: 36 outliers final: 14 residues processed: 140 average time/residue: 0.6040 time to fit residues: 89.7293 Evaluate side-chains 131 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 0.1980 chunk 32 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 340 ASN C 188 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.156166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113887 restraints weight = 10747.057| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.44 r_work: 0.2908 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9747 Z= 0.095 Angle : 0.506 11.905 13206 Z= 0.270 Chirality : 0.041 0.176 1495 Planarity : 0.004 0.051 1666 Dihedral : 4.757 57.211 1316 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.51 % Allowed : 24.56 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.24), residues: 1199 helix: 2.06 (0.27), residues: 392 sheet: 0.90 (0.29), residues: 297 loop : -1.14 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 20 TYR 0.015 0.001 TYR S 235 PHE 0.013 0.001 PHE C 189 TRP 0.012 0.001 TRP D 57 HIS 0.003 0.001 HIS D 17 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9741) covalent geometry : angle 0.50566 (13194) SS BOND : bond 0.00424 ( 6) SS BOND : angle 0.84647 ( 12) hydrogen bonds : bond 0.03814 ( 421) hydrogen bonds : angle 4.27153 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.300 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6662 (tm) REVERT: B 22 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6526 (mtm180) REVERT: B 23 LYS cc_start: 0.7566 (tppt) cc_final: 0.7224 (tptm) REVERT: B 46 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: B 175 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: B 215 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7592 (mp0) REVERT: B 217 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8427 (pmm) REVERT: B 234 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: C 5 LEU cc_start: 0.8418 (mt) cc_final: 0.8051 (mp) REVERT: S 11 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8332 (tt) REVERT: S 235 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.5646 (t80) outliers start: 26 outliers final: 12 residues processed: 129 average time/residue: 0.5940 time to fit residues: 81.4319 Evaluate side-chains 125 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 61 TYR Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 108 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 340 ASN C 188 HIS C 244 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111634 restraints weight = 10685.276| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.32 r_work: 0.2846 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9747 Z= 0.120 Angle : 0.543 12.087 13206 Z= 0.288 Chirality : 0.042 0.213 1495 Planarity : 0.004 0.049 1666 Dihedral : 4.910 59.755 1316 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.32 % Allowed : 24.95 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.24), residues: 1199 helix: 1.94 (0.27), residues: 391 sheet: 1.00 (0.29), residues: 291 loop : -1.17 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 205 TYR 0.019 0.001 TYR S 235 PHE 0.014 0.001 PHE C 189 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9741) covalent geometry : angle 0.54177 (13194) SS BOND : bond 0.00596 ( 6) SS BOND : angle 1.19037 ( 12) hydrogen bonds : bond 0.04536 ( 421) hydrogen bonds : angle 4.38196 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.532 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6721 (tm) REVERT: B 22 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6602 (mtm180) REVERT: B 23 LYS cc_start: 0.7576 (tppt) cc_final: 0.7242 (tptm) REVERT: B 46 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8099 (mtp85) REVERT: B 175 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: B 215 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7629 (mp0) REVERT: B 217 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8425 (pmm) REVERT: B 234 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8877 (m-80) REVERT: C 5 LEU cc_start: 0.8487 (mt) cc_final: 0.8114 (mp) REVERT: C 21 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8602 (ttm110) REVERT: S 11 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8374 (tt) REVERT: S 235 TYR cc_start: 0.6808 (OUTLIER) cc_final: 0.5668 (t80) outliers start: 24 outliers final: 15 residues processed: 124 average time/residue: 0.7867 time to fit residues: 103.1953 Evaluate side-chains 129 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain D residue 4 SER Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 32 optimal weight: 0.0030 chunk 65 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 340 ASN C 188 HIS S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.155103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.113469 restraints weight = 10693.379| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.11 r_work: 0.2887 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9747 Z= 0.104 Angle : 0.522 12.226 13206 Z= 0.277 Chirality : 0.042 0.194 1495 Planarity : 0.004 0.049 1666 Dihedral : 4.735 58.990 1314 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.42 % Allowed : 25.15 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.24), residues: 1199 helix: 2.05 (0.27), residues: 389 sheet: 0.94 (0.29), residues: 297 loop : -1.15 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.017 0.001 TYR S 235 PHE 0.014 0.001 PHE C 189 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9741) covalent geometry : angle 0.52112 (13194) SS BOND : bond 0.00500 ( 6) SS BOND : angle 0.98450 ( 12) hydrogen bonds : bond 0.04164 ( 421) hydrogen bonds : angle 4.33066 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3873.47 seconds wall clock time: 66 minutes 36.28 seconds (3996.28 seconds total)