Starting phenix.real_space_refine on Sat Aug 23 12:20:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gda_29944/08_2025/8gda_29944_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gda_29944/08_2025/8gda_29944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gda_29944/08_2025/8gda_29944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gda_29944/08_2025/8gda_29944.map" model { file = "/net/cci-nas-00/data/ceres_data/8gda_29944/08_2025/8gda_29944_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gda_29944/08_2025/8gda_29944_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5445 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 4881 2.51 5 N 1349 2.21 5 O 1370 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7650 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1750 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 9, 'ARG:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2477 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 12, 'GLN:plan1': 3, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 391 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "N" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 922 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2080 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YZV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.80, per 1000 atoms: 0.24 Number of scatterers: 7650 At special positions: 0 Unit cell: (95.2, 124.1, 100.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 F 2 9.00 O 1370 8.00 N 1349 7.00 C 4881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 372.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 40.1% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 32 removed outlier: 3.865A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.605A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.756A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.674A pdb=" N ASP A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 350 removed outlier: 4.134A pdb=" N ASP A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 388 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.628A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.533A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.904A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 44 removed outlier: 3.877A pdb=" N MET R 27 " --> pdb=" O ILE R 23 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE R 28 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 50 Processing helix chain 'R' and resid 52 through 83 removed outlier: 4.044A pdb=" N THR R 56 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R 57 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 88 through 123 removed outlier: 3.663A pdb=" N ILE R 110 " --> pdb=" O GLY R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 131 Processing helix chain 'R' and resid 132 through 152 removed outlier: 3.708A pdb=" N ALA R 136 " --> pdb=" O ASP R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 157 removed outlier: 3.797A pdb=" N GLY R 157 " --> pdb=" O PRO R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 206 removed outlier: 3.527A pdb=" N TYR R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER R 185 " --> pdb=" O HIS R 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE R 194 " --> pdb=" O GLY R 190 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE R 196 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 221 Processing helix chain 'R' and resid 267 through 298 removed outlier: 3.668A pdb=" N VAL R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU R 282 " --> pdb=" O SER R 278 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 305 through 309 removed outlier: 3.712A pdb=" N ASN R 309 " --> pdb=" O VAL R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 319 Processing helix chain 'R' and resid 320 through 330 Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 333 through 344 removed outlier: 3.603A pdb=" N LYS R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.771A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.662A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.978A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.583A 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: 6.630A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.601A 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 151 removed outlier: 3.696A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.527A 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: 3.589A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.705A 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: 3.718A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.956A 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: 6.648A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.556A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLY N 16 " --> pdb=" O SER N 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.142A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1089 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: 0.99 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1220 1.31 - 1.44: 2167 1.44 - 1.56: 4348 1.56 - 1.68: 2 1.68 - 1.81: 65 Bond restraints: 7802 Sorted by residual: bond pdb=" C13 YZV R 501 " pdb=" C14 YZV R 501 " ideal model delta sigma weight residual 1.525 1.221 0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C11 YZV R 501 " pdb=" N01 YZV R 501 " ideal model delta sigma weight residual 1.458 1.211 0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C15 YZV R 501 " pdb=" N01 YZV R 501 " ideal model delta sigma weight residual 1.445 1.237 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C12 YZV R 501 " pdb=" O02 YZV R 501 " ideal model delta sigma weight residual 1.420 1.300 0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C10 YZV R 501 " pdb=" C11 YZV R 501 " ideal model delta sigma weight residual 1.504 1.612 -0.108 2.00e-02 2.50e+03 2.89e+01 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 10482 2.29 - 4.58: 119 4.58 - 6.87: 19 6.87 - 9.16: 4 9.16 - 11.45: 2 Bond angle restraints: 10626 Sorted by residual: angle pdb=" C11 YZV R 501 " pdb=" N01 YZV R 501 " pdb=" C12 YZV R 501 " ideal model delta sigma weight residual 112.24 100.79 11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C09 YZV R 501 " pdb=" C08 YZV R 501 " pdb=" O01 YZV R 501 " ideal model delta sigma weight residual 114.12 103.54 10.58 3.00e+00 1.11e-01 1.24e+01 angle pdb=" C ILE R 286 " pdb=" CA ILE R 286 " pdb=" CB ILE R 286 " ideal model delta sigma weight residual 114.35 110.80 3.55 1.06e+00 8.90e-01 1.12e+01 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.11 116.67 5.44 1.64e+00 3.72e-01 1.10e+01 angle pdb=" N ILE R 23 " pdb=" CA ILE R 23 " pdb=" C ILE R 23 " ideal model delta sigma weight residual 108.88 115.97 -7.09 2.16e+00 2.14e-01 1.08e+01 ... (remaining 10621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 4160 15.96 - 31.93: 331 31.93 - 47.89: 78 47.89 - 63.86: 23 63.86 - 79.82: 10 Dihedral angle restraints: 4602 sinusoidal: 1594 harmonic: 3008 Sorted by residual: dihedral pdb=" CA GLY A 353 " pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CB CYS R 92 " pdb=" SG CYS R 92 " pdb=" SG CYS R 170 " pdb=" CB CYS R 170 " ideal model delta sinusoidal sigma weight residual 93.00 132.74 -39.74 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -117.05 31.05 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 4599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1050 0.062 - 0.123: 189 0.123 - 0.185: 10 0.185 - 0.247: 1 0.247 - 0.308: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C08 YZV R 501 " pdb=" C07 YZV R 501 " pdb=" C09 YZV R 501 " pdb=" O01 YZV R 501 " both_signs ideal model delta sigma weight residual False 2.37 2.68 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA SER R 319 " pdb=" N SER R 319 " pdb=" C SER R 319 " pdb=" CB SER R 319 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ILE R 23 " pdb=" N ILE R 23 " pdb=" C ILE R 23 " pdb=" CB ILE R 23 " both_signs ideal model delta sigma weight residual False 2.43 2.21 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1249 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 174 " 0.020 2.00e-02 2.50e+03 1.85e-02 8.59e+00 pdb=" CG TRP R 174 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP R 174 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 174 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 174 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 174 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 174 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 102 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C PHE R 102 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE R 102 " 0.011 2.00e-02 2.50e+03 pdb=" N SER R 103 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 857 2.75 - 3.28: 7297 3.28 - 3.82: 12011 3.82 - 4.36: 14062 4.36 - 4.90: 25387 Nonbonded interactions: 59614 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.207 3.040 nonbonded pdb=" O GLY A 52 " pdb=" OG1 THR A 55 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" O TYR A 339 " model vdw 2.244 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.275 3.040 nonbonded pdb=" O PHE N 29 " pdb=" NH2 ARG N 72 " model vdw 2.289 3.120 ... (remaining 59609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.580 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 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 : 0.007 0.304 7805 Z= 0.357 Angle : 0.686 11.449 10632 Z= 0.388 Chirality : 0.047 0.308 1252 Planarity : 0.004 0.040 1347 Dihedral : 13.617 79.821 2647 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.41 % Allowed : 1.09 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.27), residues: 1016 helix: 0.40 (0.27), residues: 406 sheet: -0.17 (0.35), residues: 220 loop : -1.34 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 134 TYR 0.014 0.002 TYR R 130 PHE 0.017 0.002 PHE A 376 TRP 0.050 0.003 TRP R 174 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00722 ( 7802) covalent geometry : angle 0.68623 (10626) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.79110 ( 6) hydrogen bonds : bond 0.13489 ( 375) hydrogen bonds : angle 5.91461 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6084 (mm-30) REVERT: A 24 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7499 (ttmm) REVERT: A 31 GLN cc_start: 0.7654 (tp40) cc_final: 0.7199 (tp40) REVERT: A 33 ASP cc_start: 0.7117 (t0) cc_final: 0.6695 (t0) REVERT: A 36 VAL cc_start: 0.8318 (t) cc_final: 0.7857 (p) REVERT: A 211 LYS cc_start: 0.8501 (mttm) cc_final: 0.8258 (mttm) REVERT: A 274 ASP cc_start: 0.7488 (t70) cc_final: 0.7237 (t70) REVERT: A 343 ASP cc_start: 0.7752 (m-30) cc_final: 0.7477 (m-30) REVERT: B 13 GLN cc_start: 0.6733 (pp30) cc_final: 0.6448 (pp30) REVERT: B 14 LEU cc_start: 0.7508 (mt) cc_final: 0.7171 (mm) REVERT: B 19 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7294 (ttp80) REVERT: B 46 ARG cc_start: 0.6553 (mtp-110) cc_final: 0.6211 (mtp-110) REVERT: B 66 ASP cc_start: 0.7345 (p0) cc_final: 0.6961 (p0) REVERT: B 78 LYS cc_start: 0.8491 (tppt) cc_final: 0.8084 (mmtt) REVERT: B 155 ASN cc_start: 0.8550 (t0) cc_final: 0.8124 (t0) REVERT: B 189 SER cc_start: 0.8598 (p) cc_final: 0.7968 (m) REVERT: B 233 CYS cc_start: 0.7866 (t) cc_final: 0.7075 (t) REVERT: B 239 ASN cc_start: 0.7797 (m110) cc_final: 0.7532 (m-40) REVERT: B 243 THR cc_start: 0.8307 (m) cc_final: 0.8058 (t) REVERT: B 303 ASP cc_start: 0.7418 (m-30) cc_final: 0.7126 (m-30) REVERT: B 308 LEU cc_start: 0.8107 (mt) cc_final: 0.7722 (mp) REVERT: R 27 MET cc_start: 0.7413 (mtm) cc_final: 0.7175 (mtp) REVERT: R 30 PHE cc_start: 0.8307 (m-10) cc_final: 0.7729 (m-80) REVERT: R 72 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7311 (p) REVERT: R 94 TYR cc_start: 0.7316 (t80) cc_final: 0.6968 (t80) REVERT: R 113 MET cc_start: 0.8073 (mtp) cc_final: 0.7837 (mtp) REVERT: R 184 TYR cc_start: 0.7886 (t80) cc_final: 0.6596 (t80) REVERT: R 327 TRP cc_start: 0.8880 (m100) cc_final: 0.8324 (m100) REVERT: R 331 LEU cc_start: 0.8210 (mt) cc_final: 0.7823 (mp) outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.1271 time to fit residues: 28.9007 Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 119 ASN B 176 GLN B 183 HIS N 31 ASN R 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.107262 restraints weight = 10919.640| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.35 r_work: 0.3144 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7805 Z= 0.150 Angle : 0.544 7.348 10632 Z= 0.296 Chirality : 0.042 0.152 1252 Planarity : 0.004 0.039 1347 Dihedral : 5.871 54.238 1155 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.23 % Allowed : 9.30 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.27), residues: 1016 helix: 0.76 (0.27), residues: 415 sheet: -0.04 (0.35), residues: 223 loop : -1.21 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.011 0.001 TYR R 130 PHE 0.018 0.002 PHE A 376 TRP 0.017 0.002 TRP R 174 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7802) covalent geometry : angle 0.54362 (10626) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.77601 ( 6) hydrogen bonds : bond 0.04362 ( 375) hydrogen bonds : angle 4.49360 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7927 (tp40) cc_final: 0.7620 (tp40) REVERT: A 33 ASP cc_start: 0.7494 (t0) cc_final: 0.7048 (t0) REVERT: A 46 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8476 (mp) REVERT: A 211 LYS cc_start: 0.8757 (mttm) cc_final: 0.8513 (mttm) REVERT: A 274 ASP cc_start: 0.8200 (t70) cc_final: 0.7951 (t0) REVERT: A 279 ASN cc_start: 0.8270 (t0) cc_final: 0.8047 (t0) REVERT: A 317 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7497 (mpp-170) REVERT: A 343 ASP cc_start: 0.7879 (m-30) cc_final: 0.7667 (m-30) REVERT: A 347 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7239 (ttp80) REVERT: A 390 GLN cc_start: 0.8633 (pt0) cc_final: 0.8334 (pt0) REVERT: B 13 GLN cc_start: 0.7128 (pp30) cc_final: 0.6778 (pp30) REVERT: B 14 LEU cc_start: 0.8307 (mt) cc_final: 0.7633 (mm) REVERT: B 19 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8184 (ttp80) REVERT: B 46 ARG cc_start: 0.7596 (mtp-110) cc_final: 0.7373 (mtp-110) REVERT: B 66 ASP cc_start: 0.7397 (p0) cc_final: 0.7043 (p0) REVERT: B 78 LYS cc_start: 0.8327 (tppt) cc_final: 0.8051 (mmtt) REVERT: B 155 ASN cc_start: 0.8509 (t0) cc_final: 0.8034 (t0) REVERT: B 189 SER cc_start: 0.8543 (p) cc_final: 0.7959 (m) REVERT: B 239 ASN cc_start: 0.7895 (m110) cc_final: 0.7639 (m-40) REVERT: B 307 VAL cc_start: 0.8944 (t) cc_final: 0.8144 (p) REVERT: B 308 LEU cc_start: 0.8174 (mt) cc_final: 0.7830 (mp) REVERT: G 27 ARG cc_start: 0.8833 (mtt90) cc_final: 0.8531 (mtm180) REVERT: R 30 PHE cc_start: 0.8772 (m-10) cc_final: 0.8249 (m-80) REVERT: R 54 PHE cc_start: 0.8185 (t80) cc_final: 0.7896 (t80) REVERT: R 72 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7978 (p) REVERT: R 184 TYR cc_start: 0.8358 (t80) cc_final: 0.7406 (t80) REVERT: R 331 LEU cc_start: 0.8304 (mt) cc_final: 0.7892 (mp) outliers start: 9 outliers final: 5 residues processed: 166 average time/residue: 0.0976 time to fit residues: 20.7951 Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 272 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 28 optimal weight: 0.0060 chunk 48 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108930 restraints weight = 10790.262| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.35 r_work: 0.3167 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7805 Z= 0.108 Angle : 0.488 6.808 10632 Z= 0.264 Chirality : 0.041 0.144 1252 Planarity : 0.003 0.038 1347 Dihedral : 4.988 54.258 1153 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.50 % Allowed : 12.04 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.27), residues: 1016 helix: 1.22 (0.28), residues: 409 sheet: 0.06 (0.35), residues: 225 loop : -0.93 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 265 TYR 0.009 0.001 TYR R 130 PHE 0.013 0.001 PHE A 376 TRP 0.012 0.001 TRP A 234 HIS 0.002 0.001 HIS R 129 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7802) covalent geometry : angle 0.48806 (10626) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.51764 ( 6) hydrogen bonds : bond 0.03568 ( 375) hydrogen bonds : angle 4.12243 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.297 Fit side-chains REVERT: A 17 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7630 (tmmt) REVERT: A 31 GLN cc_start: 0.7847 (tp40) cc_final: 0.7495 (tp40) REVERT: A 33 ASP cc_start: 0.7378 (t0) cc_final: 0.7060 (t0) REVERT: A 211 LYS cc_start: 0.8803 (mttm) cc_final: 0.8011 (mttm) REVERT: A 343 ASP cc_start: 0.7917 (m-30) cc_final: 0.7668 (m-30) REVERT: A 390 GLN cc_start: 0.8597 (pt0) cc_final: 0.8283 (pt0) REVERT: B 13 GLN cc_start: 0.7185 (pp30) cc_final: 0.6784 (pp30) REVERT: B 14 LEU cc_start: 0.8321 (mt) cc_final: 0.7599 (mm) REVERT: B 19 ARG cc_start: 0.8583 (ttm-80) cc_final: 0.8200 (ttp80) REVERT: B 25 CYS cc_start: 0.8197 (p) cc_final: 0.7828 (p) REVERT: B 46 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.7308 (mtp-110) REVERT: B 66 ASP cc_start: 0.7314 (p0) cc_final: 0.6944 (p0) REVERT: B 78 LYS cc_start: 0.8365 (tppt) cc_final: 0.8023 (mmtt) REVERT: B 189 SER cc_start: 0.8552 (p) cc_final: 0.7998 (m) REVERT: B 307 VAL cc_start: 0.8915 (t) cc_final: 0.8175 (p) REVERT: R 30 PHE cc_start: 0.8781 (m-10) cc_final: 0.8222 (m-80) REVERT: R 184 TYR cc_start: 0.8326 (t80) cc_final: 0.7378 (t80) outliers start: 11 outliers final: 9 residues processed: 166 average time/residue: 0.1042 time to fit residues: 21.7612 Evaluate side-chains 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 38 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN N 31 ASN R 313 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.108072 restraints weight = 11033.845| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.40 r_work: 0.3183 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7805 Z= 0.127 Angle : 0.497 7.055 10632 Z= 0.269 Chirality : 0.041 0.149 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.886 54.080 1152 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.78 % Allowed : 14.77 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.27), residues: 1016 helix: 1.40 (0.28), residues: 405 sheet: 0.11 (0.34), residues: 227 loop : -0.85 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.009 0.001 TYR R 130 PHE 0.018 0.002 PHE A 376 TRP 0.015 0.002 TRP R 174 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7802) covalent geometry : angle 0.49682 (10626) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.55730 ( 6) hydrogen bonds : bond 0.03811 ( 375) hydrogen bonds : angle 4.07573 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.170 Fit side-chains REVERT: A 17 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7618 (tmmt) REVERT: A 25 LYS cc_start: 0.8075 (ttmm) cc_final: 0.7804 (tttt) REVERT: A 31 GLN cc_start: 0.7842 (tp40) cc_final: 0.7523 (tp40) REVERT: A 33 ASP cc_start: 0.7277 (t0) cc_final: 0.6958 (t0) REVERT: A 317 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7366 (mpp-170) REVERT: A 342 ARG cc_start: 0.8215 (ttt-90) cc_final: 0.7972 (ttt-90) REVERT: A 343 ASP cc_start: 0.7951 (m-30) cc_final: 0.7610 (m-30) REVERT: A 390 GLN cc_start: 0.8591 (pt0) cc_final: 0.8304 (pt0) REVERT: B 13 GLN cc_start: 0.7259 (pp30) cc_final: 0.6821 (pp30) REVERT: B 14 LEU cc_start: 0.8346 (mt) cc_final: 0.7588 (mm) REVERT: B 19 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8202 (ttp80) REVERT: B 25 CYS cc_start: 0.8258 (p) cc_final: 0.7814 (p) REVERT: B 66 ASP cc_start: 0.7315 (p0) cc_final: 0.6942 (p0) REVERT: B 78 LYS cc_start: 0.8436 (tppt) cc_final: 0.8075 (mmtt) REVERT: B 189 SER cc_start: 0.8570 (p) cc_final: 0.7992 (m) REVERT: B 239 ASN cc_start: 0.8231 (m-40) cc_final: 0.7981 (t0) REVERT: B 307 VAL cc_start: 0.8960 (t) cc_final: 0.8273 (p) REVERT: R 30 PHE cc_start: 0.8713 (m-10) cc_final: 0.8138 (m-80) REVERT: R 94 TYR cc_start: 0.7919 (t80) cc_final: 0.7423 (t80) REVERT: R 184 TYR cc_start: 0.8359 (t80) cc_final: 0.7435 (t80) REVERT: R 313 GLN cc_start: 0.8233 (mt0) cc_final: 0.7968 (mt0) outliers start: 13 outliers final: 10 residues processed: 168 average time/residue: 0.1019 time to fit residues: 21.6515 Evaluate side-chains 174 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.105912 restraints weight = 10942.056| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.39 r_work: 0.3168 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7805 Z= 0.156 Angle : 0.525 7.369 10632 Z= 0.283 Chirality : 0.042 0.157 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.936 52.120 1152 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.46 % Allowed : 15.18 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.27), residues: 1016 helix: 1.30 (0.27), residues: 411 sheet: 0.02 (0.34), residues: 229 loop : -0.93 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.009 0.001 TYR R 130 PHE 0.020 0.002 PHE A 376 TRP 0.021 0.002 TRP R 174 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7802) covalent geometry : angle 0.52468 (10626) SS BOND : bond 0.00248 ( 3) SS BOND : angle 0.59202 ( 6) hydrogen bonds : bond 0.04128 ( 375) hydrogen bonds : angle 4.12885 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.209 Fit side-chains REVERT: A 17 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7582 (tmmt) REVERT: A 31 GLN cc_start: 0.7809 (tp40) cc_final: 0.7456 (tp40) REVERT: A 33 ASP cc_start: 0.7288 (t0) cc_final: 0.6983 (t0) REVERT: A 343 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: A 390 GLN cc_start: 0.8630 (pt0) cc_final: 0.8351 (pt0) REVERT: B 13 GLN cc_start: 0.7241 (pp30) cc_final: 0.6858 (pp30) REVERT: B 19 ARG cc_start: 0.8617 (ttm-80) cc_final: 0.8250 (ttp80) REVERT: B 25 CYS cc_start: 0.8252 (p) cc_final: 0.7844 (p) REVERT: B 66 ASP cc_start: 0.7296 (p0) cc_final: 0.6932 (p0) REVERT: B 78 LYS cc_start: 0.8419 (tppt) cc_final: 0.8159 (mmtt) REVERT: B 189 SER cc_start: 0.8575 (p) cc_final: 0.7964 (m) REVERT: B 234 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: B 307 VAL cc_start: 0.9007 (t) cc_final: 0.8355 (p) REVERT: R 30 PHE cc_start: 0.8688 (m-10) cc_final: 0.8087 (m-80) REVERT: R 313 GLN cc_start: 0.8084 (mt0) cc_final: 0.7794 (mt0) outliers start: 18 outliers final: 13 residues processed: 165 average time/residue: 0.1080 time to fit residues: 22.3922 Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.0070 chunk 86 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107656 restraints weight = 10877.906| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.36 r_work: 0.3148 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7805 Z= 0.137 Angle : 0.507 7.279 10632 Z= 0.273 Chirality : 0.042 0.160 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.838 51.873 1152 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.19 % Allowed : 16.69 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.27), residues: 1016 helix: 1.47 (0.27), residues: 415 sheet: 0.11 (0.34), residues: 223 loop : -0.94 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.009 0.001 TYR R 130 PHE 0.019 0.002 PHE R 191 TRP 0.015 0.002 TRP R 174 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7802) covalent geometry : angle 0.50717 (10626) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.54934 ( 6) hydrogen bonds : bond 0.03884 ( 375) hydrogen bonds : angle 4.07502 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7539 (tmmt) REVERT: A 31 GLN cc_start: 0.7835 (tp40) cc_final: 0.7472 (tp40) REVERT: A 33 ASP cc_start: 0.7339 (t0) cc_final: 0.7033 (t0) REVERT: A 317 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7389 (mpp-170) REVERT: A 390 GLN cc_start: 0.8607 (pt0) cc_final: 0.8326 (pt0) REVERT: B 13 GLN cc_start: 0.7238 (pp30) cc_final: 0.6840 (pp30) REVERT: B 19 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8262 (ttp80) REVERT: B 25 CYS cc_start: 0.8307 (p) cc_final: 0.7865 (p) REVERT: B 66 ASP cc_start: 0.7259 (p0) cc_final: 0.6894 (p0) REVERT: B 78 LYS cc_start: 0.8384 (tppt) cc_final: 0.8172 (mmtt) REVERT: B 189 SER cc_start: 0.8584 (p) cc_final: 0.7975 (m) REVERT: B 307 VAL cc_start: 0.8973 (t) cc_final: 0.8372 (p) REVERT: R 30 PHE cc_start: 0.8668 (m-10) cc_final: 0.8050 (m-80) REVERT: R 184 TYR cc_start: 0.8344 (t80) cc_final: 0.7577 (t80) REVERT: R 313 GLN cc_start: 0.8012 (mt0) cc_final: 0.7754 (mt0) outliers start: 16 outliers final: 12 residues processed: 161 average time/residue: 0.1129 time to fit residues: 22.7615 Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 15 optimal weight: 0.0170 chunk 7 optimal weight: 0.0000 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.107808 restraints weight = 10862.786| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.37 r_work: 0.3154 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7805 Z= 0.128 Angle : 0.501 6.908 10632 Z= 0.269 Chirality : 0.041 0.163 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.764 52.077 1152 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.60 % Allowed : 17.37 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.27), residues: 1016 helix: 1.70 (0.27), residues: 409 sheet: 0.03 (0.34), residues: 227 loop : -0.83 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.009 0.001 TYR R 130 PHE 0.016 0.001 PHE A 376 TRP 0.015 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7802) covalent geometry : angle 0.50129 (10626) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.55501 ( 6) hydrogen bonds : bond 0.03751 ( 375) hydrogen bonds : angle 4.01240 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7489 (tmmt) REVERT: A 25 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7803 (tttt) REVERT: A 31 GLN cc_start: 0.7845 (tp40) cc_final: 0.7505 (tp40) REVERT: A 33 ASP cc_start: 0.7345 (t0) cc_final: 0.7046 (t0) REVERT: A 317 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7420 (mpp-170) REVERT: A 390 GLN cc_start: 0.8589 (pt0) cc_final: 0.8311 (pt0) REVERT: B 13 GLN cc_start: 0.7218 (pp30) cc_final: 0.6839 (pp30) REVERT: B 19 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.8297 (ttp80) REVERT: B 25 CYS cc_start: 0.8351 (p) cc_final: 0.7914 (p) REVERT: B 66 ASP cc_start: 0.7245 (p0) cc_final: 0.6904 (p0) REVERT: B 78 LYS cc_start: 0.8423 (tppt) cc_final: 0.8143 (mmtt) REVERT: B 134 ARG cc_start: 0.7563 (mtp-110) cc_final: 0.7343 (mtp-110) REVERT: B 189 SER cc_start: 0.8574 (p) cc_final: 0.7971 (m) REVERT: B 307 VAL cc_start: 0.8956 (t) cc_final: 0.8370 (p) REVERT: R 30 PHE cc_start: 0.8478 (m-10) cc_final: 0.7870 (m-80) REVERT: R 184 TYR cc_start: 0.8307 (t80) cc_final: 0.7567 (t80) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.1159 time to fit residues: 23.0661 Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107291 restraints weight = 10870.563| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.35 r_work: 0.3142 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7805 Z= 0.155 Angle : 0.526 7.362 10632 Z= 0.282 Chirality : 0.042 0.171 1252 Planarity : 0.003 0.037 1347 Dihedral : 4.871 51.569 1152 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.74 % Allowed : 17.51 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.27), residues: 1016 helix: 1.69 (0.27), residues: 409 sheet: 0.08 (0.34), residues: 226 loop : -0.84 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.010 0.001 TYR R 130 PHE 0.021 0.002 PHE R 191 TRP 0.017 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7802) covalent geometry : angle 0.52560 (10626) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.60703 ( 6) hydrogen bonds : bond 0.04069 ( 375) hydrogen bonds : angle 4.08574 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.278 Fit side-chains REVERT: A 17 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7485 (tmmt) REVERT: A 31 GLN cc_start: 0.7832 (tp40) cc_final: 0.7468 (tp40) REVERT: A 33 ASP cc_start: 0.7344 (t0) cc_final: 0.7041 (t0) REVERT: A 276 ILE cc_start: 0.8455 (mt) cc_final: 0.8092 (tt) REVERT: A 317 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7374 (mpp-170) REVERT: A 343 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: A 390 GLN cc_start: 0.8615 (pt0) cc_final: 0.8330 (pt0) REVERT: B 13 GLN cc_start: 0.7231 (pp30) cc_final: 0.6839 (pp30) REVERT: B 19 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8214 (ttp80) REVERT: B 25 CYS cc_start: 0.8304 (p) cc_final: 0.7889 (p) REVERT: B 66 ASP cc_start: 0.7235 (p0) cc_final: 0.6913 (p0) REVERT: B 78 LYS cc_start: 0.8383 (tppt) cc_final: 0.8170 (mmtt) REVERT: B 134 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7412 (mtp-110) REVERT: B 187 VAL cc_start: 0.6961 (t) cc_final: 0.6586 (t) REVERT: B 189 SER cc_start: 0.8572 (p) cc_final: 0.7935 (m) REVERT: B 307 VAL cc_start: 0.8934 (t) cc_final: 0.8429 (p) REVERT: R 30 PHE cc_start: 0.8459 (m-10) cc_final: 0.7830 (m-80) REVERT: R 313 GLN cc_start: 0.7941 (mt0) cc_final: 0.7649 (mt0) outliers start: 20 outliers final: 16 residues processed: 164 average time/residue: 0.1144 time to fit residues: 23.3822 Evaluate side-chains 176 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 283 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 chunk 96 optimal weight: 0.0000 chunk 26 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.109457 restraints weight = 10762.119| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.36 r_work: 0.3200 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7805 Z= 0.106 Angle : 0.481 6.526 10632 Z= 0.258 Chirality : 0.041 0.160 1252 Planarity : 0.003 0.036 1347 Dihedral : 4.643 53.136 1152 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.33 % Allowed : 18.19 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.28), residues: 1016 helix: 1.98 (0.28), residues: 409 sheet: 0.21 (0.35), residues: 216 loop : -0.84 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.009 0.001 TYR R 130 PHE 0.012 0.001 PHE A 376 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 7802) covalent geometry : angle 0.48105 (10626) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.52357 ( 6) hydrogen bonds : bond 0.03407 ( 375) hydrogen bonds : angle 3.89614 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7436 (tmmt) REVERT: A 25 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7783 (tttt) REVERT: A 31 GLN cc_start: 0.7836 (tp40) cc_final: 0.7537 (tp40) REVERT: A 33 ASP cc_start: 0.7430 (t0) cc_final: 0.6967 (t0) REVERT: A 208 PHE cc_start: 0.8457 (m-80) cc_final: 0.8167 (m-80) REVERT: A 276 ILE cc_start: 0.8444 (mt) cc_final: 0.8070 (tt) REVERT: A 317 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7346 (mpp-170) REVERT: A 390 GLN cc_start: 0.8560 (pt0) cc_final: 0.8282 (pt0) REVERT: B 13 GLN cc_start: 0.7219 (pp30) cc_final: 0.6790 (pp30) REVERT: B 14 LEU cc_start: 0.8312 (mt) cc_final: 0.7553 (mm) REVERT: B 19 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8268 (ttp80) REVERT: B 25 CYS cc_start: 0.8310 (p) cc_final: 0.7858 (p) REVERT: B 66 ASP cc_start: 0.7232 (p0) cc_final: 0.6912 (p0) REVERT: B 78 LYS cc_start: 0.8374 (tppt) cc_final: 0.8148 (mmtt) REVERT: B 187 VAL cc_start: 0.6951 (t) cc_final: 0.6603 (t) REVERT: B 189 SER cc_start: 0.8560 (p) cc_final: 0.7944 (m) REVERT: B 307 VAL cc_start: 0.8917 (t) cc_final: 0.8448 (p) REVERT: R 30 PHE cc_start: 0.8481 (m-10) cc_final: 0.7862 (m-80) REVERT: R 184 TYR cc_start: 0.8231 (t80) cc_final: 0.7446 (t80) outliers start: 17 outliers final: 14 residues processed: 165 average time/residue: 0.1344 time to fit residues: 27.6649 Evaluate side-chains 169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 75 optimal weight: 0.0070 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107794 restraints weight = 10816.785| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.35 r_work: 0.3186 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7805 Z= 0.146 Angle : 0.520 7.063 10632 Z= 0.277 Chirality : 0.042 0.151 1252 Planarity : 0.003 0.040 1347 Dihedral : 4.766 52.130 1152 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.33 % Allowed : 18.74 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.27), residues: 1016 helix: 1.89 (0.27), residues: 409 sheet: 0.27 (0.35), residues: 215 loop : -0.90 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.009 0.001 TYR R 130 PHE 0.021 0.002 PHE R 191 TRP 0.017 0.002 TRP R 174 HIS 0.004 0.001 HIS R 129 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7802) covalent geometry : angle 0.52037 (10626) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.57020 ( 6) hydrogen bonds : bond 0.03849 ( 375) hydrogen bonds : angle 4.00250 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7487 (tmmt) REVERT: A 25 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7751 (tttt) REVERT: A 31 GLN cc_start: 0.7852 (tp40) cc_final: 0.7532 (tp40) REVERT: A 33 ASP cc_start: 0.7419 (t0) cc_final: 0.7030 (t0) REVERT: A 276 ILE cc_start: 0.8472 (mt) cc_final: 0.8096 (tt) REVERT: A 317 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7387 (mpp-170) REVERT: A 390 GLN cc_start: 0.8599 (pt0) cc_final: 0.8316 (pt0) REVERT: B 13 GLN cc_start: 0.7189 (pp30) cc_final: 0.6799 (pp30) REVERT: B 19 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8279 (ttp80) REVERT: B 25 CYS cc_start: 0.8398 (p) cc_final: 0.7965 (p) REVERT: B 66 ASP cc_start: 0.7245 (p0) cc_final: 0.6923 (p0) REVERT: B 187 VAL cc_start: 0.6994 (t) cc_final: 0.6639 (t) REVERT: B 189 SER cc_start: 0.8571 (p) cc_final: 0.7951 (m) REVERT: B 307 VAL cc_start: 0.8916 (t) cc_final: 0.8438 (p) REVERT: R 30 PHE cc_start: 0.8494 (m-10) cc_final: 0.7870 (m-80) outliers start: 17 outliers final: 13 residues processed: 159 average time/residue: 0.1226 time to fit residues: 24.4290 Evaluate side-chains 168 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 170 CYS Chi-restraints excluded: chain R residue 174 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 0.0970 chunk 91 optimal weight: 0.0980 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109945 restraints weight = 10834.799| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.34 r_work: 0.3215 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7805 Z= 0.105 Angle : 0.482 6.396 10632 Z= 0.257 Chirality : 0.041 0.142 1252 Planarity : 0.003 0.038 1347 Dihedral : 4.625 53.825 1152 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.92 % Allowed : 18.88 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.28), residues: 1016 helix: 2.08 (0.27), residues: 409 sheet: 0.20 (0.35), residues: 215 loop : -0.79 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.009 0.001 TYR R 130 PHE 0.012 0.001 PHE A 376 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 129 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7802) covalent geometry : angle 0.48155 (10626) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.50966 ( 6) hydrogen bonds : bond 0.03326 ( 375) hydrogen bonds : angle 3.87598 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1955.07 seconds wall clock time: 34 minutes 2.25 seconds (2042.25 seconds total)