Starting phenix.real_space_refine on Wed Apr 30 12:05:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3z_36869/04_2025/8k3z_36869_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3z_36869/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3z_36869/04_2025/8k3z_36869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3z_36869/04_2025/8k3z_36869.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3z_36869/04_2025/8k3z_36869_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3z_36869/04_2025/8k3z_36869_neut.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLU:plan': 1, 'ASP:plan': 3} 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: 6.10, per 1000 atoms: 0.64 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.17 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: 2.73 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- 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 : 7.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (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 TRP 0.014 0.001 TRP D 57 HIS 0.004 0.001 HIS A 79 PHE 0.012 0.001 PHE B 151 TYR 0.028 0.001 TYR S 235 ARG 0.001 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.13973 ( 421) hydrogen bonds : angle 6.04303 ( 1197) SS BOND : bond 0.00583 ( 6) SS BOND : angle 1.53563 ( 12) covalent geometry : bond 0.00314 ( 9741) covalent geometry : angle 0.62399 (13194) *********************** 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 : 1.183 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: 1.5143 time to fit residues: 224.3706 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 : 1.037 ------------------------------------------------------------------------------- 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 100 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.0270 chunk 30 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- 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** D 30 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 = 0.3649 r_free = 0.3649 target = 0.150329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107604 restraints weight = 10607.746| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.18 r_work: 0.2775 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9747 Z= 0.163 Angle : 0.590 8.242 13206 Z= 0.316 Chirality : 0.044 0.257 1495 Planarity : 0.004 0.051 1666 Dihedral : 7.013 55.078 1362 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.13 % Allowed : 21.47 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1199 helix: 1.44 (0.27), residues: 389 sheet: 0.79 (0.30), residues: 298 loop : -1.16 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.014 0.002 PHE B 151 TYR 0.025 0.002 TYR S 235 ARG 0.004 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.05672 ( 421) hydrogen bonds : angle 4.80658 ( 1197) SS BOND : bond 0.00734 ( 6) SS BOND : angle 1.30021 ( 12) covalent geometry : bond 0.00383 ( 9741) covalent geometry : angle 0.58938 (13194) *********************** 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 161 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 108 time to evaluate : 1.031 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: 0.7761 (OUTLIER) cc_final: 0.7368 (mmm-85) REVERT: A 226 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8123 (mp) REVERT: A 236 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.7021 (mttm) REVERT: B 118 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8057 (p0) REVERT: B 217 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8404 (pmm) REVERT: B 234 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8888 (m-80) REVERT: C 5 LEU cc_start: 0.8366 (mt) cc_final: 0.8059 (mp) REVERT: S 11 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8387 (tt) REVERT: S 43 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8009 (mmmm) REVERT: S 113 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8260 (mm-40) REVERT: S 235 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.6431 (t80) outliers start: 53 outliers final: 24 residues processed: 151 average time/residue: 1.3166 time to fit residues: 211.8352 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU 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 5 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 93 optimal weight: 0.0370 overall best weight: 1.0662 ------------------------------------------------------------------------------- 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** D 33 ASN G 59 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 = 0.3666 r_free = 0.3666 target = 0.151943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108835 restraints weight = 10722.594| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.30 r_work: 0.2809 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0882 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= 0.127 Angle : 0.548 8.213 13206 Z= 0.293 Chirality : 0.043 0.231 1495 Planarity : 0.004 0.048 1666 Dihedral : 5.996 54.892 1333 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.55 % Allowed : 21.86 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1199 helix: 1.59 (0.27), residues: 389 sheet: 0.77 (0.30), residues: 298 loop : -1.17 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 57 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE C 189 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 421) hydrogen bonds : angle 4.56769 ( 1197) SS BOND : bond 0.00610 ( 6) SS BOND : angle 1.11209 ( 12) covalent geometry : bond 0.00289 ( 9741) covalent geometry : angle 0.54751 (13194) *********************** 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 153 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 2.046 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: 0.7751 (OUTLIER) cc_final: 0.7398 (mmm-85) REVERT: A 226 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7927 (mp) REVERT: A 233 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: B 46 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8069 (mtp85) REVERT: B 118 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8018 (p0) REVERT: B 217 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8359 (pmm) REVERT: B 234 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: C 5 LEU cc_start: 0.8381 (mt) cc_final: 0.8050 (mp) REVERT: C 330 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6724 (mtmt) REVERT: S 11 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8384 (tt) REVERT: S 235 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.5983 (t80) outliers start: 47 outliers final: 20 residues processed: 144 average time/residue: 1.8379 time to fit residues: 280.9990 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 186 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 251 CYS Chi-restraints excluded: chain B residue 4 LEU 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 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 234 LEU 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 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.150385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108030 restraints weight = 10633.457| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.27 r_work: 0.2791 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9747 Z= 0.133 Angle : 0.554 7.605 13206 Z= 0.297 Chirality : 0.043 0.236 1495 Planarity : 0.004 0.050 1666 Dihedral : 5.542 56.125 1323 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.16 % Allowed : 22.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1199 helix: 1.66 (0.27), residues: 389 sheet: 0.75 (0.29), residues: 298 loop : -1.21 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 57 HIS 0.004 0.001 HIS A 79 PHE 0.013 0.001 PHE C 196 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 421) hydrogen bonds : angle 4.52098 ( 1197) SS BOND : bond 0.00660 ( 6) SS BOND : angle 1.17123 ( 12) covalent geometry : bond 0.00309 ( 9741) covalent geometry : angle 0.55295 (13194) *********************** 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 148 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 1.114 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: 0.7758 (OUTLIER) cc_final: 0.7348 (mmm-85) REVERT: A 188 ARG cc_start: 0.8801 (ttp-170) cc_final: 0.8499 (ttm170) REVERT: A 194 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6654 (tm) REVERT: A 226 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7944 (mp) REVERT: B 118 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8051 (p0) REVERT: B 175 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: B 217 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8380 (pmm) REVERT: B 234 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: C 5 LEU cc_start: 0.8376 (mt) cc_final: 0.8021 (mp) REVERT: C 330 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6902 (mtmt) REVERT: S 11 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8373 (tt) REVERT: S 235 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6028 (t80) outliers start: 43 outliers final: 21 residues processed: 141 average time/residue: 1.4819 time to fit residues: 221.5987 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 105 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 88 VAL 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 194 LEU 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 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 B residue 334 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.149522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107052 restraints weight = 10675.406| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.21 r_work: 0.2777 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1147 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= 0.156 Angle : 0.578 9.110 13206 Z= 0.310 Chirality : 0.044 0.264 1495 Planarity : 0.004 0.047 1666 Dihedral : 5.651 58.079 1323 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.03 % Allowed : 21.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1199 helix: 1.65 (0.27), residues: 389 sheet: 0.72 (0.29), residues: 302 loop : -1.26 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.015 0.002 PHE C 196 TYR 0.025 0.002 TYR S 235 ARG 0.004 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 421) hydrogen bonds : angle 4.58906 ( 1197) SS BOND : bond 0.00725 ( 6) SS BOND : angle 1.23778 ( 12) covalent geometry : bond 0.00369 ( 9741) covalent geometry : angle 0.57747 (13194) *********************** 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 158 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 106 time to evaluate : 1.048 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: 0.7778 (OUTLIER) cc_final: 0.7474 (mmm-85) REVERT: A 226 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7975 (mp) REVERT: B 22 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6279 (mtm180) REVERT: B 46 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8110 (mtp85) REVERT: B 118 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7990 (p0) REVERT: B 175 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: B 217 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8391 (pmm) REVERT: B 234 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8881 (m-80) REVERT: C 5 LEU cc_start: 0.8413 (mt) cc_final: 0.8025 (mp) REVERT: C 330 LYS cc_start: 0.7353 (OUTLIER) cc_final: 0.7137 (mtmt) REVERT: S 11 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8365 (tt) REVERT: S 235 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6274 (t80) outliers start: 52 outliers final: 23 residues processed: 145 average time/residue: 1.3774 time to fit residues: 212.2014 Evaluate side-chains 139 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 88 VAL 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 251 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 22 ARG 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 330 LYS 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 77 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 86 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109122 restraints weight = 10641.981| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.28 r_work: 0.2800 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1163 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= 0.121 Angle : 0.534 9.904 13206 Z= 0.286 Chirality : 0.042 0.224 1495 Planarity : 0.004 0.048 1666 Dihedral : 5.457 57.057 1323 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.77 % Allowed : 22.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1199 helix: 1.77 (0.27), residues: 392 sheet: 0.86 (0.30), residues: 294 loop : -1.20 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 57 HIS 0.003 0.001 HIS A 79 PHE 0.012 0.001 PHE C 189 TYR 0.021 0.001 TYR S 235 ARG 0.002 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 421) hydrogen bonds : angle 4.45348 ( 1197) SS BOND : bond 0.00585 ( 6) SS BOND : angle 1.02960 ( 12) covalent geometry : bond 0.00276 ( 9741) covalent geometry : angle 0.53343 (13194) *********************** 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 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.334 Fit side-chains 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: 0.7764 (OUTLIER) cc_final: 0.7464 (mmm-85) REVERT: B 22 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6210 (mtm180) REVERT: B 46 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8095 (mtp85) REVERT: B 118 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7930 (p0) REVERT: B 175 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: B 217 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8383 (pmm) REVERT: B 234 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: C 5 LEU cc_start: 0.8391 (mt) cc_final: 0.8021 (mp) REVERT: C 330 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7083 (mtmt) REVERT: S 11 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8356 (tt) REVERT: S 235 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.5868 (t80) outliers start: 39 outliers final: 17 residues processed: 141 average time/residue: 1.5553 time to fit residues: 235.0466 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 VAL Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 ASN 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 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 B residue 275 SER 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 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 64 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3669 r_free = 0.3669 target = 0.152241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.109808 restraints weight = 10686.289| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.34 r_work: 0.2807 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9747 Z= 0.116 Angle : 0.533 10.573 13206 Z= 0.285 Chirality : 0.042 0.216 1495 Planarity : 0.004 0.049 1666 Dihedral : 5.341 57.680 1320 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.77 % Allowed : 22.92 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1199 helix: 1.91 (0.27), residues: 389 sheet: 0.88 (0.29), residues: 294 loop : -1.23 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.010 0.001 HIS C 57 PHE 0.013 0.001 PHE C 189 TYR 0.020 0.001 TYR S 235 ARG 0.003 0.000 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 421) hydrogen bonds : angle 4.42484 ( 1197) SS BOND : bond 0.00581 ( 6) SS BOND : angle 1.06627 ( 12) covalent geometry : bond 0.00263 ( 9741) covalent geometry : angle 0.53194 (13194) *********************** 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 145 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 106 time to evaluate : 1.217 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: 0.7107 (OUTLIER) cc_final: 0.6605 (tm) REVERT: B 22 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6209 (mtm180) REVERT: B 46 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8109 (mtp85) REVERT: B 118 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7969 (p0) REVERT: B 175 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7824 (mp10) REVERT: B 217 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8372 (pmm) REVERT: B 234 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8833 (m-80) REVERT: C 5 LEU cc_start: 0.8440 (mt) cc_final: 0.8065 (mp) REVERT: C 330 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7073 (mtmt) REVERT: S 11 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8348 (tt) REVERT: S 235 TYR cc_start: 0.6928 (OUTLIER) cc_final: 0.5787 (t80) outliers start: 39 outliers final: 17 residues processed: 136 average time/residue: 1.5767 time to fit residues: 229.1622 Evaluate side-chains 132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 194 LEU 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 B residue 275 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 33 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 57 HIS C 188 HIS D 22 ASN S 183 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.155328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112928 restraints weight = 10814.015| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.44 r_work: 0.2890 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1334 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= 0.102 Angle : 0.512 11.140 13206 Z= 0.273 Chirality : 0.041 0.188 1495 Planarity : 0.004 0.049 1666 Dihedral : 4.969 57.295 1318 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.00 % Allowed : 23.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1199 helix: 1.97 (0.27), residues: 391 sheet: 0.92 (0.29), residues: 293 loop : -1.18 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 57 HIS 0.007 0.001 HIS C 57 PHE 0.013 0.001 PHE C 189 TYR 0.017 0.001 TYR S 235 ARG 0.003 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 421) hydrogen bonds : angle 4.31705 ( 1197) SS BOND : bond 0.00484 ( 6) SS BOND : angle 0.90531 ( 12) covalent geometry : bond 0.00226 ( 9741) covalent geometry : angle 0.51175 (13194) *********************** 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 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6677 (tm) REVERT: B 46 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8095 (mtp85) REVERT: B 175 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: B 215 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7656 (mp0) REVERT: B 217 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8415 (pmm) REVERT: B 234 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8843 (m-80) REVERT: C 5 LEU cc_start: 0.8445 (mt) cc_final: 0.8072 (mp) REVERT: S 11 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8332 (tt) REVERT: S 235 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5491 (t80) outliers start: 31 outliers final: 13 residues processed: 134 average time/residue: 1.8659 time to fit residues: 267.5528 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 : 1.339 ------------------------------------------------------------------------------- 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 4 LEU 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 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 79 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 188 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.110638 restraints weight = 10652.849| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.55 r_work: 0.2880 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1327 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= 0.122 Angle : 0.541 11.681 13206 Z= 0.288 Chirality : 0.042 0.214 1495 Planarity : 0.004 0.051 1666 Dihedral : 4.933 58.764 1316 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.90 % Allowed : 24.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1199 helix: 1.95 (0.27), residues: 389 sheet: 0.93 (0.29), residues: 293 loop : -1.20 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.014 0.001 PHE C 189 TYR 0.019 0.001 TYR S 235 ARG 0.003 0.000 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 421) hydrogen bonds : angle 4.38808 ( 1197) SS BOND : bond 0.00594 ( 6) SS BOND : angle 1.16511 ( 12) covalent geometry : bond 0.00280 ( 9741) covalent geometry : angle 0.54044 (13194) *********************** 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 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.181 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: 0.7152 (OUTLIER) cc_final: 0.6681 (tm) REVERT: B 22 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6225 (mtm180) REVERT: B 46 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8106 (mtp85) REVERT: B 118 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7970 (p0) REVERT: B 175 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7834 (mp10) REVERT: B 215 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7668 (mp0) REVERT: B 217 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8390 (pmm) REVERT: B 234 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8878 (m-80) REVERT: C 5 LEU cc_start: 0.8456 (mt) cc_final: 0.8087 (mp) REVERT: S 11 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8336 (tt) REVERT: S 235 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5724 (t80) outliers start: 30 outliers final: 15 residues processed: 131 average time/residue: 1.4504 time to fit residues: 202.1939 Evaluate side-chains 129 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 118 ASP 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 275 SER Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 181 THR 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 14 optimal weight: 0.1980 chunk 116 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 35 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.156303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114723 restraints weight = 10870.336| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.13 r_work: 0.2861 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1436 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= 0.096 Angle : 0.505 12.140 13206 Z= 0.269 Chirality : 0.041 0.171 1495 Planarity : 0.004 0.047 1666 Dihedral : 4.729 57.749 1316 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.93 % Allowed : 25.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1199 helix: 2.09 (0.27), residues: 390 sheet: 0.84 (0.29), residues: 299 loop : -1.13 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS A 79 PHE 0.013 0.001 PHE C 189 TYR 0.015 0.001 TYR S 235 ARG 0.002 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 421) hydrogen bonds : angle 4.26891 ( 1197) SS BOND : bond 0.00419 ( 6) SS BOND : angle 0.83580 ( 12) covalent geometry : bond 0.00205 ( 9741) covalent geometry : angle 0.50469 (13194) ********************** 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 127 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 1.449 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 194 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6691 (tm) REVERT: B 46 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8103 (mtp85) REVERT: B 175 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: B 215 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7633 (mp0) REVERT: B 217 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8444 (pmm) REVERT: B 234 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8839 (m-80) REVERT: C 5 LEU cc_start: 0.8442 (mt) cc_final: 0.8079 (mp) REVERT: S 11 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8333 (tt) REVERT: S 235 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.5508 (t80) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 1.7496 time to fit residues: 227.8352 Evaluate side-chains 123 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4 LEU 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 22 ASN 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 117 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN C 188 HIS D 22 ASN S 183 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.110252 restraints weight = 10708.210| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.62 r_work: 0.2818 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1393 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= 0.126 Angle : 0.543 12.139 13206 Z= 0.288 Chirality : 0.043 0.211 1495 Planarity : 0.004 0.054 1666 Dihedral : 4.784 59.452 1314 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.32 % Allowed : 25.05 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1199 helix: 1.99 (0.27), residues: 388 sheet: 0.91 (0.29), residues: 293 loop : -1.21 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 79 PHE 0.014 0.001 PHE C 189 TYR 0.018 0.001 TYR S 235 ARG 0.005 0.000 ARG D 20 Details of bonding type rmsd hydrogen bonds : bond 0.04577 ( 421) hydrogen bonds : angle 4.35742 ( 1197) SS BOND : bond 0.00618 ( 6) SS BOND : angle 1.22024 ( 12) covalent geometry : bond 0.00291 ( 9741) covalent geometry : angle 0.54180 (13194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9505.94 seconds wall clock time: 166 minutes 30.01 seconds (9990.01 seconds total)