Starting phenix.real_space_refine on Thu Jul 2 19:40:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfc_33785/07_2026/7yfc_33785.cif" } resolution = 3.0 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= 0.000 sd= 1.000 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 59 5.16 5 C 6294 2.51 5 N 1686 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9882 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1912 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1799 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain breaks: 1 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2096 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 252} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'PHE:plan': 4, 'TRP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.70, per 1000 atoms: 0.17 Number of scatterers: 9882 At special positions: 0 Unit cell: (88.88, 126.72, 127.6, 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 59 16.00 O 1843 8.00 N 1686 7.00 C 6294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 229 " distance=2.03 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 87 " - pdb=" SG CYS R 164 " 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: 0.92 Conformation dependent library (CDL) restraints added in 330.0 milliseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 34.9% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 4.004A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.592A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.567A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.287A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 4.087A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.522A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.503A pdb=" N SER C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 56 removed outlier: 3.938A pdb=" N GLY C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.990A pdb=" N VAL C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.749A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.192A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 43 Processing helix chain 'R' and resid 48 through 76 removed outlier: 4.471A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 83 through 118 Processing helix chain 'R' and resid 118 through 124 Processing helix chain 'R' and resid 131 through 155 removed outlier: 3.570A pdb=" N TRP R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 171 through 181 Processing helix chain 'R' and resid 183 through 204 Processing helix chain 'R' and resid 300 through 329 removed outlier: 4.010A pdb=" N LEU R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 4.073A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.796A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 359 through 362 removed outlier: 4.115A pdb=" N HIS R 362 " --> pdb=" O PRO R 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 359 through 362' Processing helix chain 'R' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.586A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.235A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.596A 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: 6.823A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.617A 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: 3.719A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.514A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.905A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.504A pdb=" N GLY B 244 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.687A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.769A pdb=" N MET C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 11 through 12 removed outlier: 4.407A pdb=" N PHE C 110 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.567A pdb=" N ARG C 160 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 146 through 148 removed outlier: 3.653A pdb=" N GLU C 246 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 189 " --> pdb=" O TRP C 176 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 178 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 187 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.009A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1590 1.27 - 1.40: 2602 1.40 - 1.54: 5747 1.54 - 1.68: 73 1.68 - 1.81: 85 Bond restraints: 10097 Sorted by residual: bond pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 1.492 1.218 0.274 5.00e-02 4.00e+02 2.99e+01 bond pdb=" N PRO R 355 " pdb=" CA PRO R 355 " ideal model delta sigma weight residual 1.471 1.521 -0.050 1.32e-02 5.74e+03 1.43e+01 bond pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.51e+00 bond pdb=" C3 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 10092 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.55: 13686 6.55 - 13.11: 4 13.11 - 19.66: 1 19.66 - 26.21: 0 26.21 - 32.77: 2 Bond angle restraints: 13693 Sorted by residual: angle pdb=" N PRO R 355 " pdb=" CD PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 103.20 74.58 28.62 1.50e+00 4.44e-01 3.64e+02 angle pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " ideal model delta sigma weight residual 104.50 71.73 32.77 1.90e+00 2.77e-01 2.97e+02 angle pdb=" CA PRO R 355 " pdb=" N PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 112.00 102.69 9.31 1.40e+00 5.10e-01 4.42e+01 angle pdb=" N PRO R 355 " pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sigma weight residual 103.48 97.38 6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sigma weight residual 106.10 125.14 -19.04 3.20e+00 9.77e-02 3.54e+01 ... (remaining 13688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5035 17.86 - 35.72: 692 35.72 - 53.59: 191 53.59 - 71.45: 25 71.45 - 89.31: 17 Dihedral angle restraints: 5960 sinusoidal: 2302 harmonic: 3658 Sorted by residual: dihedral pdb=" N PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " pdb=" CB PRO R 355 " ideal model delta sinusoidal sigma weight residual 30.00 91.78 -61.78 1 1.50e+01 4.44e-03 2.25e+01 dihedral pdb=" CA PRO R 355 " pdb=" CB PRO R 355 " pdb=" CG PRO R 355 " pdb=" CD PRO R 355 " ideal model delta sinusoidal sigma weight residual 38.00 104.29 -66.29 1 2.00e+01 2.50e-03 1.43e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -55.61 -30.39 1 1.00e+01 1.00e-02 1.32e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1275 0.051 - 0.102: 224 0.102 - 0.153: 42 0.153 - 0.204: 1 0.204 - 0.255: 1 Chirality restraints: 1543 Sorted by residual: chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA TYR C 235 " pdb=" N TYR C 235 " pdb=" C TYR C 235 " pdb=" CB TYR C 235 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA THR B 181 " pdb=" N THR B 181 " pdb=" C THR B 181 " pdb=" CB THR B 181 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1540 not shown) Planarity restraints: 1731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 354 " 0.037 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO R 355 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 355 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 355 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 40 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO C 41 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 235 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO C 236 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.025 5.00e-02 4.00e+02 ... (remaining 1728 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 688 2.74 - 3.28: 9272 3.28 - 3.82: 16074 3.82 - 4.36: 18907 4.36 - 4.90: 34512 Nonbonded interactions: 79453 Sorted by model distance: nonbonded pdb=" NH1 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.198 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD2 ASP B 76 " model vdw 2.239 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ASP A 335 " model vdw 2.273 3.120 nonbonded pdb=" OD1 ASP N 90 " pdb=" OH TYR N 94 " model vdw 2.279 3.040 nonbonded pdb=" NH2 ARG C 180 " pdb=" OE2 GLU C 222 " model vdw 2.297 3.120 ... (remaining 79448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.005 0.371 10102 Z= 0.169 Angle : 0.658 32.766 13703 Z= 0.356 Chirality : 0.040 0.255 1543 Planarity : 0.004 0.054 1731 Dihedral : 17.785 89.310 3589 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.09 % Allowed : 31.36 % Favored : 68.54 % 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 are not related in a simple way. whole: 1.05 (0.24), residues: 1240 helix: 2.54 (0.26), residues: 394 sheet: 0.47 (0.29), residues: 316 loop : -0.57 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 134 TYR 0.021 0.001 TYR C 235 PHE 0.015 0.001 PHE A 189 TRP 0.010 0.001 TRP R 316 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.17 (10097) covalent geometry : angle 0.65772 / 0.36 (13693) SS BOND : bond 0.00371 / 0.23 ( 5) SS BOND : angle 0.65251 / 0.39 ( 10) hydrogen bonds : bond 0.13193 / 8.89 ( 466) hydrogen bonds : angle 5.02048 / 3.46 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.378 Fit side-chains REVERT: B 42 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.7085 (tpp-160) REVERT: R 353 VAL cc_start: 0.6956 (t) cc_final: 0.6711 (p) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.5080 time to fit residues: 66.1398 Evaluate side-chains 109 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 349 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.156486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125572 restraints weight = 12404.191| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.63 r_work: 0.3374 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10102 Z= 0.109 Angle : 0.522 10.885 13703 Z= 0.272 Chirality : 0.040 0.187 1543 Planarity : 0.004 0.047 1731 Dihedral : 4.866 68.090 1386 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.04 % Allowed : 28.36 % Favored : 67.61 % 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 are not related in a simple way. whole: 1.10 (0.24), residues: 1240 helix: 2.45 (0.26), residues: 407 sheet: 0.46 (0.29), residues: 320 loop : -0.48 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.025 0.001 TYR C 235 PHE 0.015 0.001 PHE A 189 TRP 0.010 0.001 TRP B 211 HIS 0.003 0.001 HIS R 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10097) covalent geometry : angle 0.52194 / 0.27 (13693) SS BOND : bond 0.00299 / 0.19 ( 5) SS BOND : angle 0.54622 / 0.33 ( 10) hydrogen bonds : bond 0.03856 / 2.60 ( 466) hydrogen bonds : angle 4.24888 / 2.97 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 116 time to evaluate : 0.333 Fit side-chains REVERT: B 59 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: B 197 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6295 (mtp-110) REVERT: B 336 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7982 (tt) REVERT: C 169 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8498 (m110) REVERT: R 353 VAL cc_start: 0.6655 (t) cc_final: 0.6329 (p) outliers start: 43 outliers final: 14 residues processed: 142 average time/residue: 0.4729 time to fit residues: 72.5508 Evaluate side-chains 129 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 127 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.0070 chunk 21 optimal weight: 0.3980 chunk 108 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125659 restraints weight = 12381.697| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.65 r_work: 0.3395 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10102 Z= 0.107 Angle : 0.492 9.236 13703 Z= 0.257 Chirality : 0.040 0.197 1543 Planarity : 0.004 0.046 1731 Dihedral : 4.708 68.629 1384 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.07 % Allowed : 27.42 % Favored : 67.51 % 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 are not related in a simple way. whole: 1.13 (0.24), residues: 1240 helix: 2.51 (0.26), residues: 407 sheet: 0.49 (0.29), residues: 320 loop : -0.50 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.028 0.001 TYR C 235 PHE 0.036 0.001 PHE R 349 TRP 0.009 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (10097) covalent geometry : angle 0.49145 / 0.26 (13693) SS BOND : bond 0.00349 / 0.21 ( 5) SS BOND : angle 0.79004 / 0.43 ( 10) hydrogen bonds : bond 0.03656 / 2.48 ( 466) hydrogen bonds : angle 4.08851 / 2.87 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.373 Fit side-chains REVERT: B 13 GLN cc_start: 0.7793 (tp40) cc_final: 0.7577 (tp-100) REVERT: B 59 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: B 172 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7616 (tt0) REVERT: B 197 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6274 (mtp-110) REVERT: B 234 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.7587 (t80) REVERT: B 336 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 169 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8506 (m110) REVERT: R 75 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7337 (t-170) REVERT: R 353 VAL cc_start: 0.6563 (t) cc_final: 0.6248 (p) outliers start: 54 outliers final: 24 residues processed: 155 average time/residue: 0.4493 time to fit residues: 75.6025 Evaluate side-chains 142 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 195 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN N 35 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124352 restraints weight = 12435.887| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.65 r_work: 0.3367 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10102 Z= 0.121 Angle : 0.503 9.961 13703 Z= 0.262 Chirality : 0.041 0.207 1543 Planarity : 0.004 0.046 1731 Dihedral : 4.770 68.575 1384 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.35 % Allowed : 28.45 % Favored : 66.20 % 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 are not related in a simple way. whole: 1.09 (0.24), residues: 1240 helix: 2.48 (0.26), residues: 407 sheet: 0.50 (0.29), residues: 318 loop : -0.55 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.029 0.001 TYR C 235 PHE 0.015 0.001 PHE A 189 TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10097) covalent geometry : angle 0.50206 / 0.26 (13693) SS BOND : bond 0.00468 / 0.32 ( 5) SS BOND : angle 1.11487 / 0.62 ( 10) hydrogen bonds : bond 0.03672 / 2.49 ( 466) hydrogen bonds : angle 4.05472 / 2.85 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 112 time to evaluate : 0.275 Fit side-chains REVERT: B 59 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: B 172 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7622 (tt0) REVERT: B 197 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6325 (mtp-110) REVERT: B 234 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 336 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8022 (tt) REVERT: C 169 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8539 (m110) REVERT: R 75 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7336 (t-170) REVERT: R 353 VAL cc_start: 0.6572 (t) cc_final: 0.6252 (p) outliers start: 57 outliers final: 29 residues processed: 153 average time/residue: 0.4245 time to fit residues: 70.6608 Evaluate side-chains 142 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 195 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 63 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 259 GLN C 183 GLN N 35 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127432 restraints weight = 12381.717| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.63 r_work: 0.3414 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10102 Z= 0.092 Angle : 0.476 10.009 13703 Z= 0.248 Chirality : 0.040 0.191 1543 Planarity : 0.003 0.045 1731 Dihedral : 4.588 68.397 1384 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.04 % Allowed : 29.48 % Favored : 66.48 % 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 are not related in a simple way. whole: 1.21 (0.24), residues: 1240 helix: 2.60 (0.26), residues: 407 sheet: 0.59 (0.29), residues: 313 loop : -0.51 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 134 TYR 0.026 0.001 TYR C 235 PHE 0.033 0.001 PHE R 349 TRP 0.009 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (10097) covalent geometry : angle 0.47555 / 0.25 (13693) SS BOND : bond 0.00316 / 0.21 ( 5) SS BOND : angle 0.60706 / 0.35 ( 10) hydrogen bonds : bond 0.03236 / 2.19 ( 466) hydrogen bonds : angle 3.88387 / 2.72 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 121 time to evaluate : 0.234 Fit side-chains REVERT: B 13 GLN cc_start: 0.7786 (tp40) cc_final: 0.7460 (mt0) REVERT: B 59 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: B 197 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6300 (mtp-110) REVERT: B 234 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.7579 (t80) REVERT: B 336 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7825 (tt) REVERT: C 230 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7514 (ttt) REVERT: R 75 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7356 (t-170) REVERT: R 353 VAL cc_start: 0.6494 (t) cc_final: 0.6245 (p) outliers start: 43 outliers final: 24 residues processed: 152 average time/residue: 0.4653 time to fit residues: 76.5114 Evaluate side-chains 141 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 195 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.156944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.126040 restraints weight = 12414.109| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.63 r_work: 0.3397 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10102 Z= 0.110 Angle : 0.495 10.019 13703 Z= 0.257 Chirality : 0.040 0.199 1543 Planarity : 0.004 0.047 1731 Dihedral : 4.682 68.670 1384 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.07 % Allowed : 29.30 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.24), residues: 1240 helix: 2.55 (0.26), residues: 407 sheet: 0.56 (0.29), residues: 313 loop : -0.54 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 134 TYR 0.028 0.001 TYR C 235 PHE 0.015 0.001 PHE A 189 TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10097) covalent geometry : angle 0.49463 / 0.26 (13693) SS BOND : bond 0.00291 / 0.18 ( 5) SS BOND : angle 0.61906 / 0.35 ( 10) hydrogen bonds : bond 0.03458 / 2.34 ( 466) hydrogen bonds : angle 3.93228 / 2.76 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.384 Fit side-chains REVERT: B 13 GLN cc_start: 0.7816 (tp40) cc_final: 0.7498 (mt0) REVERT: B 59 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: B 172 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7652 (tt0) REVERT: B 197 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6324 (mtp-110) REVERT: B 234 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7575 (t80) REVERT: B 245 SER cc_start: 0.8669 (p) cc_final: 0.8216 (t) REVERT: B 336 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7968 (tt) REVERT: C 169 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8517 (m110) REVERT: C 230 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7582 (ttt) REVERT: R 75 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7361 (t-170) REVERT: R 353 VAL cc_start: 0.6610 (t) cc_final: 0.6368 (p) outliers start: 54 outliers final: 31 residues processed: 151 average time/residue: 0.3910 time to fit residues: 64.6665 Evaluate side-chains 148 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 268 ASN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122582 restraints weight = 12443.933| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.64 r_work: 0.3342 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10102 Z= 0.151 Angle : 0.541 9.813 13703 Z= 0.282 Chirality : 0.042 0.222 1543 Planarity : 0.004 0.047 1731 Dihedral : 4.980 69.031 1384 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.16 % Allowed : 29.77 % Favored : 65.07 % 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 are not related in a simple way. whole: 1.01 (0.24), residues: 1240 helix: 2.46 (0.26), residues: 405 sheet: 0.37 (0.29), residues: 318 loop : -0.57 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.033 0.002 TYR C 235 PHE 0.033 0.001 PHE R 349 TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (10097) covalent geometry : angle 0.54120 / 0.28 (13693) SS BOND : bond 0.00409 / 0.26 ( 5) SS BOND : angle 0.76170 / 0.41 ( 10) hydrogen bonds : bond 0.03974 / 2.69 ( 466) hydrogen bonds : angle 4.12397 / 2.90 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 109 time to evaluate : 0.385 Fit side-chains REVERT: B 59 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: B 172 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7647 (tt0) REVERT: B 197 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6281 (mtp-110) REVERT: B 234 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.7608 (t80) REVERT: B 336 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8129 (tt) REVERT: C 169 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8676 (m110) REVERT: C 214 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7391 (tp) REVERT: C 230 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7629 (ttt) REVERT: G 47 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7998 (mt-10) REVERT: R 63 PHE cc_start: 0.6704 (m-10) cc_final: 0.6340 (m-10) REVERT: R 75 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7275 (t-170) REVERT: R 301 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5661 (tp) REVERT: R 353 VAL cc_start: 0.6591 (t) cc_final: 0.6292 (p) outliers start: 55 outliers final: 30 residues processed: 149 average time/residue: 0.4700 time to fit residues: 76.3785 Evaluate side-chains 144 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 110 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124194 restraints weight = 12435.356| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.66 r_work: 0.3373 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10102 Z= 0.119 Angle : 0.516 10.041 13703 Z= 0.269 Chirality : 0.041 0.237 1543 Planarity : 0.004 0.053 1731 Dihedral : 4.858 68.780 1384 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.04 % Allowed : 31.08 % Favored : 64.88 % 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 are not related in a simple way. whole: 1.07 (0.24), residues: 1240 helix: 2.52 (0.26), residues: 407 sheet: 0.37 (0.29), residues: 318 loop : -0.54 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.032 0.001 TYR C 235 PHE 0.016 0.001 PHE A 189 TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10097) covalent geometry : angle 0.51615 / 0.27 (13693) SS BOND : bond 0.00319 / 0.20 ( 5) SS BOND : angle 0.60925 / 0.34 ( 10) hydrogen bonds : bond 0.03616 / 2.45 ( 466) hydrogen bonds : angle 4.04953 / 2.85 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.399 Fit side-chains REVERT: B 13 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: B 59 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: B 172 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7637 (tt0) REVERT: B 197 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6249 (mtp-110) REVERT: B 234 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 245 SER cc_start: 0.8790 (p) cc_final: 0.8313 (t) REVERT: B 336 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8023 (tt) REVERT: C 169 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8603 (m110) REVERT: C 230 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7561 (ttt) REVERT: R 75 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7216 (t-170) REVERT: R 301 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5582 (tp) outliers start: 43 outliers final: 32 residues processed: 143 average time/residue: 0.4829 time to fit residues: 75.0906 Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.154904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123556 restraints weight = 12386.032| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.65 r_work: 0.3355 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10102 Z= 0.132 Angle : 0.531 9.973 13703 Z= 0.276 Chirality : 0.041 0.247 1543 Planarity : 0.004 0.059 1731 Dihedral : 4.904 68.911 1384 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.69 % Allowed : 30.52 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1240 helix: 2.49 (0.26), residues: 407 sheet: 0.37 (0.29), residues: 318 loop : -0.55 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.032 0.001 TYR C 235 PHE 0.049 0.001 PHE R 349 TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10097) covalent geometry : angle 0.53089 / 0.28 (13693) SS BOND : bond 0.00347 / 0.22 ( 5) SS BOND : angle 0.61869 / 0.34 ( 10) hydrogen bonds : bond 0.03727 / 2.53 ( 466) hydrogen bonds : angle 4.07263 / 2.86 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 109 time to evaluate : 0.389 Fit side-chains REVERT: B 59 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: B 172 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7621 (tt0) REVERT: B 197 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6262 (mtp-110) REVERT: B 234 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7559 (t80) REVERT: B 245 SER cc_start: 0.8841 (p) cc_final: 0.8329 (t) REVERT: B 336 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8044 (tt) REVERT: C 169 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8629 (m110) REVERT: C 230 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7650 (ttt) REVERT: R 75 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.7170 (t-170) REVERT: R 301 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5593 (tp) outliers start: 50 outliers final: 35 residues processed: 146 average time/residue: 0.4306 time to fit residues: 68.6524 Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124273 restraints weight = 12312.275| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.62 r_work: 0.3372 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10102 Z= 0.128 Angle : 0.531 10.000 13703 Z= 0.276 Chirality : 0.041 0.251 1543 Planarity : 0.004 0.060 1731 Dihedral : 4.897 68.928 1384 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.32 % Allowed : 31.08 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1240 helix: 2.51 (0.26), residues: 407 sheet: 0.37 (0.29), residues: 318 loop : -0.54 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 134 TYR 0.031 0.001 TYR C 235 PHE 0.016 0.001 PHE A 189 TRP 0.012 0.001 TRP N 47 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10097) covalent geometry : angle 0.53094 / 0.28 (13693) SS BOND : bond 0.00341 / 0.21 ( 5) SS BOND : angle 0.61075 / 0.33 ( 10) hydrogen bonds : bond 0.03686 / 2.50 ( 466) hydrogen bonds : angle 4.07764 / 2.87 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.250 Fit side-chains REVERT: A 310 LYS cc_start: 0.7613 (tptp) cc_final: 0.7055 (tptt) REVERT: B 13 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7389 (mt0) REVERT: B 59 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: B 172 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7628 (tt0) REVERT: B 197 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6270 (mtp-110) REVERT: B 234 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.7571 (t80) REVERT: B 245 SER cc_start: 0.8797 (p) cc_final: 0.8333 (t) REVERT: B 336 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8017 (tt) REVERT: C 169 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8620 (m110) REVERT: C 230 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7540 (ttt) REVERT: N 30 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8497 (p) REVERT: R 75 HIS cc_start: 0.7507 (OUTLIER) cc_final: 0.7147 (t-170) REVERT: R 301 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5629 (tp) outliers start: 46 outliers final: 35 residues processed: 146 average time/residue: 0.4378 time to fit residues: 69.6524 Evaluate side-chains 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 169 ASN Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 235 TYR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 42 VAL Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 75 HIS Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 127 THR Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.0370 chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 26 optimal weight: 0.0050 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 75 optimal weight: 0.5980 overall best weight: 0.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN C 183 GLN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123961 restraints weight = 12406.813| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.64 r_work: 0.3371 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 10102 Z= 0.234 Angle : 0.841 59.200 13703 Z= 0.495 Chirality : 0.046 0.795 1543 Planarity : 0.004 0.056 1731 Dihedral : 4.899 68.926 1384 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.32 % Allowed : 31.27 % Favored : 64.41 % Cbeta Deviations : 0.08 % 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 are not related in a simple way. whole: 1.04 (0.24), residues: 1240 helix: 2.48 (0.26), residues: 407 sheet: 0.37 (0.29), residues: 318 loop : -0.54 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.031 0.001 TYR C 235 PHE 0.016 0.001 PHE A 189 TRP 0.012 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.23 (10097) covalent geometry : angle 0.84116 / 0.50 (13693) SS BOND : bond 0.00298 / 0.18 ( 5) SS BOND : angle 0.59291 / 0.32 ( 10) hydrogen bonds : bond 0.03642 / 2.47 ( 466) hydrogen bonds : angle 4.08692 / 2.87 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.48 seconds wall clock time: 54 minutes 54.83 seconds (3294.83 seconds total)