Starting phenix.real_space_refine on Sun May 11 17:27:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3q_39751/05_2025/8z3q_39751.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3q_39751/05_2025/8z3q_39751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3q_39751/05_2025/8z3q_39751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3q_39751/05_2025/8z3q_39751.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3q_39751/05_2025/8z3q_39751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3q_39751/05_2025/8z3q_39751.cif" } resolution = 2.76 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= 0.001 sd= 0.020 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 48 5.16 5 C 5282 2.51 5 N 1429 2.21 5 O 1518 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8277 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1841 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2462 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 355 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1710 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1909 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 11, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 147 Time building chain proxies: 5.36, per 1000 atoms: 0.65 Number of scatterers: 8277 At special positions: 0 Unit cell: (89.3, 120.65, 128.25, 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 48 16.00 O 1518 8.00 N 1429 7.00 C 5282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.00 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: 2.03 Conformation dependent library (CDL) restraints added in 1.3 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 36.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.542A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.537A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.574A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.569A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.607A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.762A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.619A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.141A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.548A pdb=" N SER R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.517A pdb=" N CYS R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 69 removed outlier: 3.930A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 78 removed outlier: 4.336A pdb=" N TRP R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 99 removed outlier: 4.018A pdb=" N ILE R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE R 97 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 121 removed outlier: 3.796A pdb=" N ILE R 105 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 180 through 188 removed outlier: 4.419A pdb=" N VAL R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 3.956A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 251 Proline residue: R 239 - end of helix removed outlier: 3.903A pdb=" N ILE R 250 " --> pdb=" O SER R 246 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 275 removed outlier: 3.589A pdb=" N HIS R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 272 " --> pdb=" O TYR R 268 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA R 273 " --> pdb=" O HIS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 291 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 4.901A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.707A 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: 3.901A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.759A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.757A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.656A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.822A 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: 6.667A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.020A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.653A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.672A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.618A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE S 216 " --> pdb=" O VAL S 155 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.735A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1182 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: 2.50 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1489 1.33 - 1.45: 2283 1.45 - 1.57: 4618 1.57 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 8457 Sorted by residual: bond pdb=" CA ALA B 106 " pdb=" C ALA B 106 " ideal model delta sigma weight residual 1.528 1.470 0.058 1.18e-02 7.18e+03 2.41e+01 bond pdb=" CA ALA A 7 " pdb=" C ALA A 7 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.29e-02 6.01e+03 2.29e+01 bond pdb=" CA ALA A 12 " pdb=" CB ALA A 12 " ideal model delta sigma weight residual 1.534 1.474 0.060 1.45e-02 4.76e+03 1.72e+01 bond pdb=" N SER S 145 " pdb=" CA SER S 145 " ideal model delta sigma weight residual 1.459 1.413 0.046 1.16e-02 7.43e+03 1.57e+01 bond pdb=" CA ASP A 9 " pdb=" C ASP A 9 " ideal model delta sigma weight residual 1.521 1.476 0.045 1.29e-02 6.01e+03 1.24e+01 ... (remaining 8452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 11351 2.23 - 4.46: 142 4.46 - 6.69: 35 6.69 - 8.92: 6 8.92 - 11.16: 4 Bond angle restraints: 11538 Sorted by residual: angle pdb=" N ALA A 12 " pdb=" CA ALA A 12 " pdb=" C ALA A 12 " ideal model delta sigma weight residual 113.88 102.72 11.16 1.23e+00 6.61e-01 8.23e+01 angle pdb=" N ILE A 382 " pdb=" CA ILE A 382 " pdb=" C ILE A 382 " ideal model delta sigma weight residual 111.81 104.65 7.16 8.60e-01 1.35e+00 6.93e+01 angle pdb=" N LYS A 10 " pdb=" CA LYS A 10 " pdb=" C LYS A 10 " ideal model delta sigma weight residual 112.26 103.03 9.23 1.32e+00 5.74e-01 4.89e+01 angle pdb=" N ALA A 11 " pdb=" CA ALA A 11 " pdb=" C ALA A 11 " ideal model delta sigma weight residual 113.19 103.79 9.40 1.58e+00 4.01e-01 3.54e+01 angle pdb=" N GLY S 152 " pdb=" CA GLY S 152 " pdb=" C GLY S 152 " ideal model delta sigma weight residual 115.27 123.34 -8.07 1.41e+00 5.03e-01 3.27e+01 ... (remaining 11533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4370 17.78 - 35.56: 440 35.56 - 53.34: 101 53.34 - 71.12: 18 71.12 - 88.89: 3 Dihedral angle restraints: 4932 sinusoidal: 1670 harmonic: 3262 Sorted by residual: dihedral pdb=" C SER A 6 " pdb=" N SER A 6 " pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta harmonic sigma weight residual -122.60 -110.39 -12.21 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " pdb=" OD1 ASP B 258 " ideal model delta sinusoidal sigma weight residual -30.00 -88.76 58.76 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 4929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1064 0.051 - 0.102: 232 0.102 - 0.153: 47 0.153 - 0.203: 6 0.203 - 0.254: 1 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA SER S 146 " pdb=" N SER S 146 " pdb=" C SER S 146 " pdb=" CB SER S 146 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ALA B 104 " pdb=" N ALA B 104 " pdb=" C ALA B 104 " pdb=" CB ALA B 104 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA SER A 6 " pdb=" N SER A 6 " pdb=" C SER A 6 " pdb=" CB SER A 6 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 1347 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 379 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" C CYS A 379 " 0.052 2.00e-02 2.50e+03 pdb=" O CYS A 379 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 380 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 8 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLU A 8 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU A 8 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP A 9 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 70 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO R 71 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " -0.027 5.00e-02 4.00e+02 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 774 2.74 - 3.28: 7598 3.28 - 3.82: 13211 3.82 - 4.36: 14751 4.36 - 4.90: 26995 Nonbonded interactions: 63329 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.205 3.040 nonbonded pdb=" ND2 ASN A 50 " pdb=" OD2 ASP A 262 " model vdw 2.225 3.120 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 261 " model vdw 2.262 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OD1 ASP B 186 " model vdw 2.268 3.120 nonbonded pdb=" O THR B 164 " pdb=" OG1 THR B 164 " model vdw 2.285 3.040 ... (remaining 63324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.360 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.004 0.062 8458 Z= 0.271 Angle : 0.679 11.156 11540 Z= 0.417 Chirality : 0.044 0.254 1350 Planarity : 0.004 0.048 1467 Dihedral : 15.336 88.895 2825 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.24 % Allowed : 24.23 % Favored : 74.54 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.78 % 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: 0.45 (0.26), residues: 1104 helix: 1.85 (0.28), residues: 384 sheet: 0.32 (0.31), residues: 294 loop : -1.17 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 244 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE R 95 TYR 0.019 0.001 TYR R 66 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.20818 ( 413) hydrogen bonds : angle 6.59540 ( 1182) SS BOND : bond 0.03367 ( 1) SS BOND : angle 3.17413 ( 2) covalent geometry : bond 0.00415 ( 8457) covalent geometry : angle 0.67759 (11538) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7869 (p) REVERT: A 381 ASP cc_start: 0.8187 (t0) cc_final: 0.7853 (t0) REVERT: B 325 MET cc_start: 0.8306 (mmt) cc_final: 0.8099 (mtp) REVERT: S 93 MET cc_start: 0.8514 (ttp) cc_final: 0.8193 (ttp) REVERT: R 32 LEU cc_start: 0.8635 (mt) cc_final: 0.8429 (mm) REVERT: R 66 TYR cc_start: 0.7550 (t80) cc_final: 0.7250 (t80) REVERT: R 237 PHE cc_start: 0.8496 (m-10) cc_final: 0.8258 (m-10) outliers start: 10 outliers final: 1 residues processed: 191 average time/residue: 0.9914 time to fit residues: 203.0068 Evaluate side-chains 179 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain S residue 147 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 237 GLN B 75 GLN B 88 ASN B 110 ASN B 119 ASN B 125 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102959 restraints weight = 12100.837| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.87 r_work: 0.3257 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8458 Z= 0.198 Angle : 0.613 8.870 11540 Z= 0.326 Chirality : 0.044 0.135 1350 Planarity : 0.005 0.052 1467 Dihedral : 4.502 29.378 1209 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.58 % Allowed : 21.88 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1104 helix: 2.01 (0.27), residues: 383 sheet: 0.44 (0.30), residues: 293 loop : -1.21 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 244 HIS 0.007 0.001 HIS S 35 PHE 0.019 0.002 PHE B 151 TYR 0.016 0.002 TYR R 66 ARG 0.005 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.06187 ( 413) hydrogen bonds : angle 4.61013 ( 1182) SS BOND : bond 0.00913 ( 1) SS BOND : angle 1.11516 ( 2) covalent geometry : bond 0.00468 ( 8457) covalent geometry : angle 0.61269 (11538) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.986 Fit side-chains REVERT: A 221 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8118 (mtmm) REVERT: A 381 ASP cc_start: 0.8326 (t0) cc_final: 0.8090 (t0) REVERT: A 394 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8093 (pt) REVERT: B 304 ARG cc_start: 0.8644 (ttm-80) cc_final: 0.8432 (ttm-80) REVERT: B 325 MET cc_start: 0.8572 (mmt) cc_final: 0.8303 (mtp) REVERT: S 67 ARG cc_start: 0.8647 (mtm110) cc_final: 0.8344 (mtp180) REVERT: R 65 LEU cc_start: 0.8391 (tt) cc_final: 0.8132 (mp) REVERT: R 66 TYR cc_start: 0.7762 (t80) cc_final: 0.7437 (t80) outliers start: 29 outliers final: 15 residues processed: 208 average time/residue: 1.0139 time to fit residues: 225.8725 Evaluate side-chains 204 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 96 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 237 GLN A 294 GLN B 75 GLN B 88 ASN B 110 ASN B 125 ASN B 155 ASN B 230 ASN B 259 GLN B 340 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.123054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.104642 restraints weight = 12281.559| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.89 r_work: 0.3282 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8458 Z= 0.130 Angle : 0.528 5.930 11540 Z= 0.283 Chirality : 0.041 0.133 1350 Planarity : 0.004 0.045 1467 Dihedral : 4.164 16.932 1207 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.71 % Allowed : 22.99 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.63 (0.26), residues: 1104 helix: 2.10 (0.27), residues: 385 sheet: 0.54 (0.31), residues: 275 loop : -1.21 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG A 238 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 413) hydrogen bonds : angle 4.26186 ( 1182) SS BOND : bond 0.00255 ( 1) SS BOND : angle 1.48779 ( 2) covalent geometry : bond 0.00295 ( 8457) covalent geometry : angle 0.52721 (11538) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.861 Fit side-chains REVERT: A 221 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8175 (mtmm) REVERT: A 258 VAL cc_start: 0.8821 (p) cc_final: 0.8551 (t) REVERT: A 381 ASP cc_start: 0.8355 (t0) cc_final: 0.8112 (t70) REVERT: B 259 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: B 304 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8380 (ttm-80) REVERT: S 4 LEU cc_start: 0.8361 (mt) cc_final: 0.8153 (tp) REVERT: S 93 MET cc_start: 0.8604 (ttp) cc_final: 0.8355 (ttp) REVERT: R 65 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8177 (mp) REVERT: R 66 TYR cc_start: 0.7712 (t80) cc_final: 0.7361 (t80) outliers start: 30 outliers final: 14 residues processed: 199 average time/residue: 1.0080 time to fit residues: 214.8422 Evaluate side-chains 197 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 105 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN B 75 GLN B 88 ASN B 110 ASN B 119 ASN B 125 ASN B 230 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.122678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.104330 restraints weight = 12264.200| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.88 r_work: 0.3285 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8458 Z= 0.125 Angle : 0.522 5.893 11540 Z= 0.279 Chirality : 0.041 0.133 1350 Planarity : 0.004 0.044 1467 Dihedral : 4.129 16.698 1207 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.20 % Allowed : 22.99 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.26), residues: 1104 helix: 2.16 (0.27), residues: 385 sheet: 0.61 (0.31), residues: 273 loop : -1.21 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.013 0.001 TYR S 190 ARG 0.002 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 413) hydrogen bonds : angle 4.15843 ( 1182) SS BOND : bond 0.00943 ( 1) SS BOND : angle 1.57743 ( 2) covalent geometry : bond 0.00285 ( 8457) covalent geometry : angle 0.52210 (11538) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.946 Fit side-chains REVERT: A 221 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8171 (mtmm) REVERT: A 258 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8549 (t) REVERT: B 49 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7598 (mtt-85) REVERT: B 304 ARG cc_start: 0.8638 (ttm-80) cc_final: 0.8409 (ttm-80) REVERT: S 93 MET cc_start: 0.8617 (ttp) cc_final: 0.8371 (ttp) REVERT: R 65 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8193 (mp) REVERT: R 66 TYR cc_start: 0.7711 (t80) cc_final: 0.7295 (t80) REVERT: R 129 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7829 (ttm110) outliers start: 34 outliers final: 19 residues processed: 200 average time/residue: 0.9997 time to fit residues: 214.3640 Evaluate side-chains 202 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 65 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 17 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN B 75 GLN B 88 ASN B 110 ASN B 125 ASN B 230 ASN B 239 ASN B 259 GLN S 171 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102230 restraints weight = 12034.447| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.85 r_work: 0.3243 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8458 Z= 0.195 Angle : 0.581 6.930 11540 Z= 0.312 Chirality : 0.043 0.135 1350 Planarity : 0.004 0.041 1467 Dihedral : 4.422 17.222 1207 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.82 % Allowed : 22.25 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.26), residues: 1104 helix: 2.03 (0.28), residues: 386 sheet: 0.50 (0.30), residues: 285 loop : -1.17 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.002 PHE B 151 TYR 0.016 0.002 TYR R 66 ARG 0.005 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.05959 ( 413) hydrogen bonds : angle 4.34360 ( 1182) SS BOND : bond 0.01253 ( 1) SS BOND : angle 1.91468 ( 2) covalent geometry : bond 0.00466 ( 8457) covalent geometry : angle 0.58002 (11538) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.856 Fit side-chains REVERT: A 10 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8533 (mtpm) REVERT: A 221 LYS cc_start: 0.8569 (mtmm) cc_final: 0.8160 (mtmm) REVERT: A 293 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8434 (mmtp) REVERT: A 394 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8098 (pt) REVERT: B 49 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7671 (mtt-85) REVERT: B 259 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: B 325 MET cc_start: 0.8621 (mmt) cc_final: 0.8385 (mtp) REVERT: S 67 ARG cc_start: 0.8627 (mtm110) cc_final: 0.8371 (mtp180) REVERT: R 66 TYR cc_start: 0.7873 (t80) cc_final: 0.7464 (t80) outliers start: 39 outliers final: 22 residues processed: 201 average time/residue: 1.0198 time to fit residues: 218.8577 Evaluate side-chains 213 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.0050 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN B 75 GLN B 230 ASN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.122139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.103957 restraints weight = 12153.568| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.85 r_work: 0.3277 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8458 Z= 0.127 Angle : 0.538 7.416 11540 Z= 0.284 Chirality : 0.041 0.133 1350 Planarity : 0.004 0.041 1467 Dihedral : 4.200 16.591 1207 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.96 % Allowed : 23.73 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.70 (0.26), residues: 1104 helix: 2.11 (0.28), residues: 388 sheet: 0.61 (0.30), residues: 278 loop : -1.17 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR S 190 ARG 0.002 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 413) hydrogen bonds : angle 4.12463 ( 1182) SS BOND : bond 0.00927 ( 1) SS BOND : angle 1.72497 ( 2) covalent geometry : bond 0.00291 ( 8457) covalent geometry : angle 0.53753 (11538) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.995 Fit side-chains REVERT: A 221 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8194 (mtmm) REVERT: B 49 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7604 (mtt-85) REVERT: B 259 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: S 67 ARG cc_start: 0.8602 (mtm110) cc_final: 0.8388 (mtp180) REVERT: S 192 MET cc_start: 0.8313 (ttp) cc_final: 0.8062 (ttp) REVERT: R 66 TYR cc_start: 0.7811 (t80) cc_final: 0.7377 (t80) outliers start: 32 outliers final: 21 residues processed: 199 average time/residue: 1.0917 time to fit residues: 231.5058 Evaluate side-chains 205 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 294 GLN B 75 GLN B 230 ASN B 239 ASN B 259 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.102734 restraints weight = 12086.592| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.86 r_work: 0.3252 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8458 Z= 0.175 Angle : 0.572 6.946 11540 Z= 0.305 Chirality : 0.043 0.134 1350 Planarity : 0.004 0.039 1467 Dihedral : 4.342 16.712 1207 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.96 % Allowed : 24.72 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.68 (0.26), residues: 1104 helix: 2.09 (0.28), residues: 388 sheet: 0.52 (0.30), residues: 284 loop : -1.15 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.015 0.002 TYR R 66 ARG 0.003 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.05518 ( 413) hydrogen bonds : angle 4.22297 ( 1182) SS BOND : bond 0.01151 ( 1) SS BOND : angle 1.96063 ( 2) covalent geometry : bond 0.00417 ( 8457) covalent geometry : angle 0.57183 (11538) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.877 Fit side-chains REVERT: A 221 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8174 (mtmm) REVERT: B 49 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7645 (mtt-85) REVERT: B 325 MET cc_start: 0.8605 (mmt) cc_final: 0.8380 (mtp) REVERT: S 67 ARG cc_start: 0.8603 (mtm110) cc_final: 0.8379 (mtp180) REVERT: R 66 TYR cc_start: 0.7893 (t80) cc_final: 0.7425 (t80) outliers start: 32 outliers final: 25 residues processed: 194 average time/residue: 1.0865 time to fit residues: 224.6938 Evaluate side-chains 211 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 97 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 294 GLN B 75 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.121586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103284 restraints weight = 12294.568| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.88 r_work: 0.3260 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8458 Z= 0.152 Angle : 0.552 6.549 11540 Z= 0.293 Chirality : 0.042 0.134 1350 Planarity : 0.004 0.039 1467 Dihedral : 4.270 16.745 1207 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.96 % Allowed : 24.10 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.71 (0.26), residues: 1104 helix: 2.17 (0.28), residues: 386 sheet: 0.55 (0.30), residues: 284 loop : -1.20 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.013 0.001 TYR A 37 ARG 0.003 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 413) hydrogen bonds : angle 4.14945 ( 1182) SS BOND : bond 0.01017 ( 1) SS BOND : angle 1.85160 ( 2) covalent geometry : bond 0.00358 ( 8457) covalent geometry : angle 0.55105 (11538) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.928 Fit side-chains REVERT: A 221 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8189 (mtmm) REVERT: B 49 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.7648 (mtt-85) REVERT: B 325 MET cc_start: 0.8588 (mmt) cc_final: 0.8321 (mtp) REVERT: S 67 ARG cc_start: 0.8611 (mtm110) cc_final: 0.8398 (mtp180) REVERT: S 192 MET cc_start: 0.8320 (ttp) cc_final: 0.8080 (ttp) REVERT: R 66 TYR cc_start: 0.7888 (t80) cc_final: 0.7417 (t80) outliers start: 32 outliers final: 23 residues processed: 199 average time/residue: 1.0684 time to fit residues: 227.6588 Evaluate side-chains 208 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 294 GLN B 75 GLN B 230 ASN B 239 ASN R 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.120788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102540 restraints weight = 12325.150| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.86 r_work: 0.3256 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8458 Z= 0.162 Angle : 0.569 6.729 11540 Z= 0.302 Chirality : 0.043 0.134 1350 Planarity : 0.004 0.042 1467 Dihedral : 4.310 16.238 1207 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.71 % Allowed : 24.23 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.72 (0.26), residues: 1104 helix: 2.16 (0.28), residues: 388 sheet: 0.60 (0.30), residues: 290 loop : -1.24 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.014 0.001 TYR A 37 ARG 0.003 0.000 ARG R 115 Details of bonding type rmsd hydrogen bonds : bond 0.05298 ( 413) hydrogen bonds : angle 4.14750 ( 1182) SS BOND : bond 0.01080 ( 1) SS BOND : angle 1.94751 ( 2) covalent geometry : bond 0.00385 ( 8457) covalent geometry : angle 0.56853 (11538) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 1.022 Fit side-chains REVERT: A 221 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8191 (mtmm) REVERT: B 49 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7631 (mtt-85) REVERT: B 325 MET cc_start: 0.8590 (mmt) cc_final: 0.8324 (mtp) REVERT: S 34 MET cc_start: 0.8544 (mmt) cc_final: 0.8228 (mmt) REVERT: S 67 ARG cc_start: 0.8607 (mtm110) cc_final: 0.8394 (mtp180) REVERT: S 192 MET cc_start: 0.8334 (ttp) cc_final: 0.8112 (ttp) REVERT: R 66 TYR cc_start: 0.7890 (t80) cc_final: 0.7390 (t80) outliers start: 30 outliers final: 25 residues processed: 193 average time/residue: 1.1736 time to fit residues: 240.9394 Evaluate side-chains 209 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 17 optimal weight: 0.0060 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 85 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN A 237 GLN A 294 GLN B 75 GLN B 230 ASN B 239 ASN B 259 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103975 restraints weight = 12266.946| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.87 r_work: 0.3277 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8458 Z= 0.127 Angle : 0.535 6.739 11540 Z= 0.284 Chirality : 0.041 0.133 1350 Planarity : 0.004 0.045 1467 Dihedral : 4.138 16.435 1207 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.83 % Allowed : 24.10 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.77 (0.26), residues: 1104 helix: 2.22 (0.28), residues: 388 sheet: 0.57 (0.30), residues: 300 loop : -1.22 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR S 190 ARG 0.007 0.000 ARG S 180 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 413) hydrogen bonds : angle 4.01358 ( 1182) SS BOND : bond 0.00835 ( 1) SS BOND : angle 1.82140 ( 2) covalent geometry : bond 0.00292 ( 8457) covalent geometry : angle 0.53481 (11538) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.962 Fit side-chains REVERT: A 10 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8607 (mtpm) REVERT: A 221 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8199 (mtmm) REVERT: B 49 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7584 (mtt-85) REVERT: B 325 MET cc_start: 0.8565 (mmt) cc_final: 0.8365 (mtp) REVERT: S 67 ARG cc_start: 0.8588 (mtm110) cc_final: 0.8377 (mtp180) REVERT: R 66 TYR cc_start: 0.7841 (t80) cc_final: 0.7418 (t80) outliers start: 31 outliers final: 27 residues processed: 191 average time/residue: 1.1255 time to fit residues: 229.0773 Evaluate side-chains 208 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 ARG Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 38 ARG Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 243 THR Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 17 optimal weight: 0.0050 chunk 65 optimal weight: 0.6980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 223 GLN B 75 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.103609 restraints weight = 12348.873| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.88 r_work: 0.3270 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8458 Z= 0.136 Angle : 0.549 7.354 11540 Z= 0.290 Chirality : 0.042 0.132 1350 Planarity : 0.004 0.045 1467 Dihedral : 4.157 16.815 1207 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.20 % Allowed : 23.61 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.77 (0.26), residues: 1104 helix: 2.18 (0.27), residues: 390 sheet: 0.63 (0.30), residues: 295 loop : -1.22 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.013 0.001 TYR A 37 ARG 0.007 0.000 ARG S 180 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 413) hydrogen bonds : angle 4.03687 ( 1182) SS BOND : bond 0.00881 ( 1) SS BOND : angle 1.82278 ( 2) covalent geometry : bond 0.00317 ( 8457) covalent geometry : angle 0.54866 (11538) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7436.18 seconds wall clock time: 128 minutes 4.78 seconds (7684.78 seconds total)