Starting phenix.real_space_refine on Sat Aug 23 05:20:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfc_33785/08_2025/7yfc_33785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfc_33785/08_2025/7yfc_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_33785/08_2025/7yfc_33785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfc_33785/08_2025/7yfc_33785.map" model { file = "/net/cci-nas-00/data/ceres_data/7yfc_33785/08_2025/7yfc_33785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfc_33785/08_2025/7yfc_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-2.0-5787/lib/python3.9/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: 2.35, per 1000 atoms: 0.24 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: 0.89 Conformation dependent library (CDL) restraints added in 356.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 1.58 Time building geometry restraints manager: 1.09 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 - 22.39: 5332 22.39 - 44.78: 585 44.78 - 67.17: 75 67.17 - 89.56: 22 89.56 - 111.95: 2 Dihedral angle restraints: 6016 sinusoidal: 2358 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=" C2 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" C5 CLR R 602 " ideal model delta sinusoidal sigma weight residual -55.03 56.92 -111.95 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C5 CLR R 602 " pdb=" C3 CLR R 602 " pdb=" C4 CLR R 602 " pdb=" O1 CLR R 602 " ideal model delta sinusoidal sigma weight residual 175.64 64.31 111.33 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 6013 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: 2.160 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 18.014 111.951 3645 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 aren 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 covalent geometry : bond 0.00518 (10097) covalent geometry : angle 0.65772 (13693) SS BOND : bond 0.00371 ( 5) SS BOND : angle 0.65251 ( 10) hydrogen bonds : bond 0.13193 ( 466) hydrogen bonds : angle 5.02048 ( 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 : 0.374 Fit side-chains REVERT: B 42 ARG cc_start: 0.7413 (mmp-170) cc_final: 0.7086 (tpp-160) REVERT: R 353 VAL cc_start: 0.6955 (t) cc_final: 0.6711 (p) outliers start: 1 outliers final: 1 residues processed: 121 average time/residue: 0.6285 time to fit residues: 81.5449 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 : 0.382 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3826 r_free = 0.3826 target = 0.156674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125784 restraints weight = 12421.458| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.63 r_work: 0.3391 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0707 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 : 0.529 11.143 13703 Z= 0.273 Chirality : 0.040 0.185 1543 Planarity : 0.004 0.047 1731 Dihedral : 5.336 45.262 1442 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.04 % Allowed : 28.45 % 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 aren not related in a simple way. whole: 1.10 (0.24), residues: 1240 helix: 2.46 (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 0.010 0.000 ARG B 134 TYR 0.026 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 A 324 Details of bonding type rmsd covalent geometry : bond 0.00237 (10097) covalent geometry : angle 0.52891 (13693) SS BOND : bond 0.00300 ( 5) SS BOND : angle 0.55576 ( 10) hydrogen bonds : bond 0.03903 ( 466) hydrogen bonds : angle 4.24901 ( 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 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.385 Fit side-chains REVERT: B 59 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: B 197 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6298 (mtp-110) REVERT: B 336 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7988 (tt) REVERT: C 169 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8498 (m110) REVERT: R 353 VAL cc_start: 0.6616 (t) cc_final: 0.6280 (p) outliers start: 43 outliers final: 14 residues processed: 143 average time/residue: 0.5832 time to fit residues: 89.6218 Evaluate side-chains 128 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 0.0770 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 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: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN N 35 ASN ** R 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.154878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123633 restraints weight = 12418.635| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.64 r_work: 0.3370 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0929 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= 0.132 Angle : 0.516 9.139 13703 Z= 0.271 Chirality : 0.041 0.215 1543 Planarity : 0.004 0.046 1731 Dihedral : 4.854 39.489 1440 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.54 % Allowed : 27.51 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.24), residues: 1240 helix: 2.42 (0.26), residues: 407 sheet: 0.46 (0.29), residues: 319 loop : -0.56 (0.27), residues: 514 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 0.035 0.001 PHE R 349 TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00305 (10097) covalent geometry : angle 0.51570 (13693) SS BOND : bond 0.00556 ( 5) SS BOND : angle 1.03687 ( 10) hydrogen bonds : bond 0.03955 ( 466) hydrogen bonds : angle 4.18381 ( 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: 59 poor density : 113 time to evaluate : 0.445 Fit side-chains REVERT: A 294 GLU cc_start: 0.6466 (tm-30) cc_final: 0.6082 (tm-30) REVERT: B 13 GLN cc_start: 0.7829 (tp40) cc_final: 0.7624 (tp-100) REVERT: B 59 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.6888 (m-80) REVERT: B 172 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7651 (tt0) REVERT: B 197 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6333 (mtp-110) REVERT: B 234 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7595 (t80) REVERT: B 336 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8060 (tt) REVERT: C 169 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8578 (m110) REVERT: C 230 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7610 (ttt) REVERT: R 75 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7341 (t-170) REVERT: R 353 VAL cc_start: 0.6591 (t) cc_final: 0.6259 (p) outliers start: 59 outliers final: 27 residues processed: 158 average time/residue: 0.5211 time to fit residues: 89.1815 Evaluate side-chains 145 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR 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 120 ILE 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 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 123 ARG Chi-restraints excluded: chain R residue 127 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3819 r_free = 0.3819 target = 0.156196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125031 restraints weight = 12419.477| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.65 r_work: 0.3385 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0999 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= 0.107 Angle : 0.489 10.109 13703 Z= 0.256 Chirality : 0.040 0.200 1543 Planarity : 0.003 0.046 1731 Dihedral : 4.653 37.334 1440 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.79 % Allowed : 28.73 % 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 aren not related in a simple way. whole: 1.12 (0.24), residues: 1240 helix: 2.51 (0.26), residues: 407 sheet: 0.46 (0.29), residues: 320 loop : -0.51 (0.27), 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 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00239 (10097) covalent geometry : angle 0.48856 (13693) SS BOND : bond 0.00354 ( 5) SS BOND : angle 0.74561 ( 10) hydrogen bonds : bond 0.03558 ( 466) hydrogen bonds : angle 4.04941 ( 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: 51 poor density : 118 time to evaluate : 0.387 Fit side-chains REVERT: B 13 GLN cc_start: 0.7752 (tp40) cc_final: 0.7552 (tp-100) REVERT: B 59 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: B 172 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7632 (tt0) REVERT: B 197 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.6313 (mtp-110) REVERT: B 234 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 336 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7984 (tt) REVERT: C 169 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8523 (m110) REVERT: C 214 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7771 (tp) REVERT: C 230 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7593 (ttt) REVERT: R 75 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7327 (t-170) REVERT: R 349 PHE cc_start: 0.7148 (t80) cc_final: 0.6797 (t80) REVERT: R 353 VAL cc_start: 0.6604 (t) cc_final: 0.6322 (p) outliers start: 51 outliers final: 27 residues processed: 152 average time/residue: 0.5665 time to fit residues: 92.8609 Evaluate side-chains 146 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 154 ASP 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 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 C residue 235 TYR 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 195 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 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 = 0.3819 r_free = 0.3819 target = 0.156210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124966 restraints weight = 12397.263| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.65 r_work: 0.3387 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1076 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= 0.110 Angle : 0.491 10.114 13703 Z= 0.256 Chirality : 0.040 0.197 1543 Planarity : 0.004 0.046 1731 Dihedral : 4.650 37.603 1440 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 5.07 % Allowed : 29.20 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.24), residues: 1240 helix: 2.53 (0.26), residues: 407 sheet: 0.44 (0.29), residues: 320 loop : -0.49 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.027 0.001 TYR C 235 PHE 0.015 0.001 PHE A 189 TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00247 (10097) covalent geometry : angle 0.49068 (13693) SS BOND : bond 0.00328 ( 5) SS BOND : angle 0.64597 ( 10) hydrogen bonds : bond 0.03528 ( 466) hydrogen bonds : angle 3.99212 ( 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 169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 115 time to evaluate : 0.397 Fit side-chains REVERT: B 59 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.6937 (m-80) REVERT: B 197 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6327 (mtp-110) REVERT: B 234 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7565 (t80) REVERT: B 336 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8003 (tt) REVERT: C 169 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8534 (m110) REVERT: C 230 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7558 (ttt) REVERT: R 75 HIS cc_start: 0.7635 (OUTLIER) cc_final: 0.7350 (t-170) REVERT: R 353 VAL cc_start: 0.6578 (t) cc_final: 0.6201 (p) outliers start: 54 outliers final: 31 residues processed: 152 average time/residue: 0.4743 time to fit residues: 78.3461 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 : 0.331 ------------------------------------------------------------------------------- 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 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 C residue 235 TYR 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 195 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 89 optimal weight: 0.2980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3838 r_free = 0.3838 target = 0.157988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127071 restraints weight = 12379.885| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.64 r_work: 0.3408 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1153 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= 0.094 Angle : 0.479 10.209 13703 Z= 0.250 Chirality : 0.040 0.209 1543 Planarity : 0.003 0.046 1731 Dihedral : 4.504 37.437 1440 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.41 % Allowed : 29.95 % 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 aren not related in a simple way. whole: 1.24 (0.24), residues: 1240 helix: 2.61 (0.26), residues: 407 sheet: 0.55 (0.29), residues: 318 loop : -0.45 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 134 TYR 0.026 0.001 TYR C 235 PHE 0.033 0.001 PHE R 349 TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00202 (10097) covalent geometry : angle 0.47942 (13693) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.52993 ( 10) hydrogen bonds : bond 0.03234 ( 466) hydrogen bonds : angle 3.88062 ( 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 165 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.464 Fit side-chains REVERT: A 310 LYS cc_start: 0.7671 (tptt) cc_final: 0.7361 (tptt) REVERT: B 13 GLN cc_start: 0.7767 (tp40) cc_final: 0.7477 (mt0) REVERT: B 59 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.6984 (m-80) REVERT: B 172 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7560 (tt0) REVERT: B 197 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6282 (mtp-110) REVERT: B 234 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.7616 (t80) REVERT: B 336 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7859 (tt) REVERT: C 169 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8461 (m110) REVERT: C 230 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7533 (ttt) REVERT: R 75 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.7324 (t-170) REVERT: R 353 VAL cc_start: 0.6522 (t) cc_final: 0.6266 (p) outliers start: 47 outliers final: 23 residues processed: 153 average time/residue: 0.5004 time to fit residues: 83.2952 Evaluate side-chains 143 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3816 r_free = 0.3816 target = 0.155851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124791 restraints weight = 12438.453| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.64 r_work: 0.3371 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1195 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= 0.124 Angle : 0.511 9.965 13703 Z= 0.266 Chirality : 0.041 0.221 1543 Planarity : 0.004 0.049 1731 Dihedral : 4.680 37.977 1440 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.69 % Allowed : 30.61 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.24), residues: 1240 helix: 2.54 (0.26), residues: 405 sheet: 0.45 (0.29), residues: 319 loop : -0.48 (0.27), residues: 516 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 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00286 (10097) covalent geometry : angle 0.51047 (13693) SS BOND : bond 0.00410 ( 5) SS BOND : angle 0.63223 ( 10) hydrogen bonds : bond 0.03608 ( 466) hydrogen bonds : angle 3.99352 ( 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 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 0.402 Fit side-chains REVERT: B 13 GLN cc_start: 0.7781 (tp40) cc_final: 0.7451 (mt0) REVERT: B 59 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: B 172 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7608 (tt0) REVERT: B 197 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6235 (mtp-110) REVERT: B 234 PHE cc_start: 0.8823 (OUTLIER) cc_final: 0.7609 (t80) REVERT: B 245 SER cc_start: 0.8758 (p) cc_final: 0.8278 (t) REVERT: B 336 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8022 (tt) REVERT: C 169 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8539 (m110) REVERT: C 230 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7587 (ttt) REVERT: R 75 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7375 (t-170) REVERT: R 301 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5578 (tp) REVERT: R 353 VAL cc_start: 0.6578 (t) cc_final: 0.6321 (p) outliers start: 50 outliers final: 32 residues processed: 149 average time/residue: 0.4958 time to fit residues: 80.0907 Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 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 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 G residue 37 LEU Chi-restraints excluded: chain N residue 48 VAL 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 123 ARG 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: 0.0670 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3822 r_free = 0.3822 target = 0.156367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125221 restraints weight = 12437.519| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.66 r_work: 0.3386 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1224 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 : 0.498 10.080 13703 Z= 0.259 Chirality : 0.041 0.237 1543 Planarity : 0.004 0.054 1731 Dihedral : 4.638 38.220 1440 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.23 % Allowed : 31.17 % 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 aren not related in a simple way. whole: 1.18 (0.24), residues: 1240 helix: 2.56 (0.26), residues: 407 sheet: 0.40 (0.29), residues: 320 loop : -0.41 (0.27), residues: 513 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 0.040 0.001 PHE R 349 TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00249 (10097) covalent geometry : angle 0.49769 (13693) SS BOND : bond 0.00293 ( 5) SS BOND : angle 0.56651 ( 10) hydrogen bonds : bond 0.03451 ( 466) hydrogen bonds : angle 3.95915 ( 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: 45 poor density : 110 time to evaluate : 0.382 Fit side-chains REVERT: B 59 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.7009 (m-80) REVERT: B 172 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7594 (tt0) REVERT: B 197 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6232 (mtp-110) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7604 (t80) REVERT: B 245 SER cc_start: 0.8734 (p) cc_final: 0.8231 (t) REVERT: B 336 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7994 (tt) REVERT: C 169 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8535 (m110) REVERT: C 230 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7589 (ttt) REVERT: N 30 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8485 (p) REVERT: R 75 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7327 (t-170) REVERT: R 301 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5562 (tp) outliers start: 45 outliers final: 32 residues processed: 143 average time/residue: 0.5055 time to fit residues: 78.3711 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 : 0.385 ------------------------------------------------------------------------------- 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 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 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 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 45 LEU Chi-restraints excluded: chain N residue 48 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 116 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 47 optimal weight: 0.0000 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 overall best weight: 0.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN R 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.129461 restraints weight = 12310.952| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.61 r_work: 0.3428 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10102 Z= 0.088 Angle : 0.480 10.256 13703 Z= 0.251 Chirality : 0.040 0.240 1543 Planarity : 0.004 0.054 1731 Dihedral : 4.406 37.828 1440 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.10 % Allowed : 32.39 % Favored : 64.51 % 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 aren not related in a simple way. whole: 1.32 (0.24), residues: 1240 helix: 2.68 (0.26), residues: 407 sheet: 0.55 (0.29), residues: 318 loop : -0.36 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 134 TYR 0.026 0.001 TYR C 235 PHE 0.014 0.001 PHE A 189 TRP 0.011 0.001 TRP N 47 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00181 (10097) covalent geometry : angle 0.47992 (13693) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.44649 ( 10) hydrogen bonds : bond 0.02997 ( 466) hydrogen bonds : angle 3.79748 ( 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 151 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.410 Fit side-chains REVERT: B 59 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: B 172 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7491 (tt0) REVERT: B 234 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7604 (t80) REVERT: B 245 SER cc_start: 0.8609 (p) cc_final: 0.8118 (t) REVERT: C 230 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7523 (ttt) REVERT: N 30 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (p) REVERT: R 75 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7262 (t-170) outliers start: 33 outliers final: 17 residues processed: 141 average time/residue: 0.4965 time to fit residues: 75.4857 Evaluate side-chains 131 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 45 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 102 optimal weight: 0.0570 chunk 118 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN G 24 ASN N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124242 restraints weight = 12256.280| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.62 r_work: 0.3375 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1308 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= 0.138 Angle : 0.543 9.984 13703 Z= 0.281 Chirality : 0.042 0.246 1543 Planarity : 0.004 0.061 1731 Dihedral : 4.725 38.659 1440 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.29 % Allowed : 32.77 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.24), residues: 1240 helix: 2.53 (0.26), residues: 407 sheet: 0.46 (0.29), residues: 318 loop : -0.43 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 134 TYR 0.034 0.001 TYR C 235 PHE 0.044 0.001 PHE R 349 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00325 (10097) covalent geometry : angle 0.54309 (13693) SS BOND : bond 0.00345 ( 5) SS BOND : angle 0.61681 ( 10) hydrogen bonds : bond 0.03698 ( 466) hydrogen bonds : angle 4.04843 ( 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 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.378 Fit side-chains REVERT: A 310 LYS cc_start: 0.7601 (tptp) cc_final: 0.7043 (tptt) REVERT: B 13 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: B 46 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6786 (mmp-170) REVERT: B 59 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: B 172 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7587 (tt0) REVERT: B 234 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7568 (t80) REVERT: C 169 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8569 (m110) REVERT: C 230 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7585 (ttt) REVERT: N 30 SER cc_start: 0.8863 (OUTLIER) cc_final: 0.8491 (p) REVERT: R 75 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7167 (t-170) REVERT: R 301 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5636 (tp) outliers start: 35 outliers final: 20 residues processed: 138 average time/residue: 0.5129 time to fit residues: 76.6090 Evaluate side-chains 139 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL 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 40 VAL Chi-restraints excluded: chain B residue 46 ARG 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 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 334 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 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 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 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.0770 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 75 optimal weight: 0.0670 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 183 GLN G 24 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 = 0.155301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124320 restraints weight = 12380.036| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.63 r_work: 0.3360 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 10102 Z= 0.213 Angle : 0.847 59.048 13703 Z= 0.495 Chirality : 0.045 0.690 1543 Planarity : 0.004 0.058 1731 Dihedral : 4.731 38.693 1440 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.29 % Allowed : 32.77 % Favored : 63.94 % 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 aren not related in a simple way. whole: 1.15 (0.24), residues: 1240 helix: 2.49 (0.26), residues: 407 sheet: 0.45 (0.29), residues: 318 loop : -0.43 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 134 TYR 0.032 0.001 TYR C 235 PHE 0.030 0.001 PHE R 349 TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00440 (10097) covalent geometry : angle 0.84665 (13693) SS BOND : bond 0.00291 ( 5) SS BOND : angle 0.60630 ( 10) hydrogen bonds : bond 0.03630 ( 466) hydrogen bonds : angle 4.05491 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.54 seconds wall clock time: 59 minutes 21.87 seconds (3561.87 seconds total)