Starting phenix.real_space_refine on Sat Aug 23 01:25:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwk_37891/08_2025/8wwk_37891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwk_37891/08_2025/8wwk_37891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwk_37891/08_2025/8wwk_37891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwk_37891/08_2025/8wwk_37891.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwk_37891/08_2025/8wwk_37891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwk_37891/08_2025/8wwk_37891.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.087 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 68 5.16 5 C 5712 2.51 5 N 1519 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 8967 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1749 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 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: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "L" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 139 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.69, per 1000 atoms: 0.19 Number of scatterers: 8967 At special positions: 0 Unit cell: (88.81, 117.7, 120.91, 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 68 16.00 O 1668 8.00 N 1519 7.00 C 5712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " 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: 0.69 Conformation dependent library (CDL) restraints added in 230.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 38.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.572A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.289A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.920A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.663A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.317A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'R' and resid 108 through 138 removed outlier: 3.573A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix removed outlier: 3.819A pdb=" N SER R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 164 Processing helix chain 'R' and resid 164 through 174 removed outlier: 5.108A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 3.892A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.725A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.824A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 302 Processing helix chain 'R' and resid 313 through 348 Proline residue: R 340 - end of helix Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.027A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.317A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.804A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.570A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.797A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.170A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.873A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.095A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.759A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.164A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.545A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.505A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.141A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 251 through 255 Processing sheet with id=AB7, first strand: chain 'L' and resid 8 through 9 485 hydrogen bonds defined for protein. 1329 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: 1.14 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2888 1.34 - 1.46: 2186 1.46 - 1.58: 3985 1.58 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 9158 Sorted by residual: bond pdb=" N GLY B 116 " pdb=" CA GLY B 116 " ideal model delta sigma weight residual 1.458 1.447 0.010 9.20e-03 1.18e+04 1.30e+00 bond pdb=" C LEU A 39 " pdb=" N GLY A 40 " ideal model delta sigma weight residual 1.331 1.320 0.010 1.46e-02 4.69e+03 4.70e-01 bond pdb=" C GLY B 116 " pdb=" O GLY B 116 " ideal model delta sigma weight residual 1.239 1.234 0.005 8.50e-03 1.38e+04 3.64e-01 bond pdb=" C MET R 165 " pdb=" N PRO R 166 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.28e-02 6.10e+03 3.18e-01 bond pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 1.502 1.515 -0.013 2.30e-02 1.89e+03 3.12e-01 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 12233 1.17 - 2.33: 148 2.33 - 3.50: 34 3.50 - 4.67: 7 4.67 - 5.84: 5 Bond angle restraints: 12427 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.88e+00 angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 109.34 112.83 -3.49 2.08e+00 2.31e-01 2.82e+00 angle pdb=" CA LEU B 190 " pdb=" CB LEU B 190 " pdb=" CG LEU B 190 " ideal model delta sigma weight residual 116.30 122.14 -5.84 3.50e+00 8.16e-02 2.78e+00 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.16 114.03 -2.87 1.76e+00 3.23e-01 2.65e+00 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 124.82 127.34 -2.52 1.78e+00 3.16e-01 2.01e+00 ... (remaining 12422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 5228 16.13 - 32.25: 166 32.25 - 48.38: 28 48.38 - 64.50: 6 64.50 - 80.63: 1 Dihedral angle restraints: 5429 sinusoidal: 2063 harmonic: 3366 Sorted by residual: dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LYS R 139 " pdb=" C LYS R 139 " pdb=" N LEU R 140 " pdb=" CA LEU R 140 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.08e+00 dihedral pdb=" N LYS A 312 " pdb=" CA LYS A 312 " pdb=" CB LYS A 312 " pdb=" CG LYS A 312 " ideal model delta sinusoidal sigma weight residual 180.00 -127.96 -52.04 3 1.50e+01 4.44e-03 9.08e+00 ... (remaining 5426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 875 0.026 - 0.051: 316 0.051 - 0.077: 136 0.077 - 0.102: 63 0.102 - 0.128: 36 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1423 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 106 " 0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO E 107 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO E 107 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.018 5.00e-02 4.00e+02 2.77e-02 1.22e+00 pdb=" N PRO B 194 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.016 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 782 2.74 - 3.28: 8784 3.28 - 3.82: 15448 3.82 - 4.36: 19349 4.36 - 4.90: 32640 Nonbonded interactions: 77003 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.242 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.283 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.291 3.040 ... (remaining 76998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 : 0.002 0.017 9162 Z= 0.075 Angle : 0.392 5.837 12435 Z= 0.207 Chirality : 0.039 0.128 1426 Planarity : 0.003 0.050 1570 Dihedral : 8.406 80.627 3245 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.72 % Allowed : 2.58 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.11 (0.25), residues: 1144 helix: 1.16 (0.25), residues: 394 sheet: 0.97 (0.30), residues: 288 loop : 0.36 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 224 TYR 0.010 0.001 TYR E 190 PHE 0.009 0.001 PHE B 199 TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00152 ( 9158) covalent geometry : angle 0.39179 (12427) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.56807 ( 8) hydrogen bonds : bond 0.23641 ( 472) hydrogen bonds : angle 7.28709 ( 1329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.327 Fit side-chains REVERT: A 8 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 10 LYS cc_start: 0.8813 (mttt) cc_final: 0.8530 (mtmp) REVERT: A 29 LYS cc_start: 0.8064 (tttt) cc_final: 0.7657 (ttpp) REVERT: B 25 CYS cc_start: 0.7906 (p) cc_final: 0.6766 (m) REVERT: B 130 GLU cc_start: 0.8313 (mp0) cc_final: 0.8105 (mp0) REVERT: C 21 MET cc_start: 0.7082 (mmm) cc_final: 0.6469 (tmt) REVERT: C 47 GLU cc_start: 0.7999 (pt0) cc_final: 0.7741 (mp0) REVERT: E 43 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8073 (mtmt) REVERT: E 77 ASN cc_start: 0.8277 (m-40) cc_final: 0.7925 (m-40) REVERT: E 223 ASP cc_start: 0.8634 (m-30) cc_final: 0.8395 (m-30) REVERT: R 142 TRP cc_start: 0.6869 (m-90) cc_final: 0.5954 (m100) REVERT: R 252 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6406 (mpp-170) outliers start: 7 outliers final: 5 residues processed: 190 average time/residue: 0.5989 time to fit residues: 120.8479 Evaluate side-chains 147 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 220 GLN B 259 GLN R 194 ASN R 281 GLN R 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128678 restraints weight = 8744.526| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.70 r_work: 0.3032 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9162 Z= 0.146 Angle : 0.532 5.771 12435 Z= 0.290 Chirality : 0.042 0.138 1426 Planarity : 0.004 0.054 1570 Dihedral : 5.121 55.630 1267 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.99 % Allowed : 7.53 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.46 (0.25), residues: 1144 helix: 2.26 (0.25), residues: 394 sheet: 0.58 (0.29), residues: 279 loop : 0.19 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 303 TYR 0.012 0.002 TYR R 341 PHE 0.013 0.002 PHE B 151 TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9158) covalent geometry : angle 0.53151 (12427) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.70598 ( 8) hydrogen bonds : bond 0.05414 ( 472) hydrogen bonds : angle 4.97057 ( 1329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.396 Fit side-chains REVERT: A 28 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: A 29 LYS cc_start: 0.8184 (tttt) cc_final: 0.7674 (ttpp) REVERT: A 33 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: B 170 ASP cc_start: 0.8982 (t70) cc_final: 0.8744 (t70) REVERT: B 217 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8453 (pmm) REVERT: E 23 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.7880 (p) REVERT: E 43 LYS cc_start: 0.8629 (mmtm) cc_final: 0.7904 (mtmt) REVERT: E 77 ASN cc_start: 0.8319 (m-40) cc_final: 0.7852 (m-40) REVERT: E 160 ARG cc_start: 0.7540 (mtp-110) cc_final: 0.7253 (ttm170) REVERT: R 142 TRP cc_start: 0.6920 (m-90) cc_final: 0.5815 (m100) REVERT: R 165 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.8004 (ttt) REVERT: R 187 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7146 (mm) REVERT: R 235 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7784 (mp) REVERT: R 252 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.5888 (mpp-170) REVERT: R 345 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7565 (tp40) outliers start: 29 outliers final: 10 residues processed: 160 average time/residue: 0.6077 time to fit residues: 102.7574 Evaluate side-chains 162 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN E 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.167332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129246 restraints weight = 8758.527| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.73 r_work: 0.3029 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9162 Z= 0.137 Angle : 0.509 5.699 12435 Z= 0.276 Chirality : 0.042 0.144 1426 Planarity : 0.004 0.056 1570 Dihedral : 5.207 58.448 1267 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.20 % Allowed : 9.39 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.46 (0.25), residues: 1144 helix: 2.49 (0.25), residues: 393 sheet: 0.42 (0.30), residues: 274 loop : 0.09 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 322 TYR 0.014 0.001 TYR R 341 PHE 0.013 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9158) covalent geometry : angle 0.50849 (12427) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.73398 ( 8) hydrogen bonds : bond 0.04795 ( 472) hydrogen bonds : angle 4.73716 ( 1329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: A 29 LYS cc_start: 0.8127 (tttt) cc_final: 0.7608 (ttpp) REVERT: A 33 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: B 217 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8431 (pmm) REVERT: C 58 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: E 23 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7854 (p) REVERT: E 43 LYS cc_start: 0.8619 (mmtm) cc_final: 0.7885 (mtmt) REVERT: E 77 ASN cc_start: 0.8375 (m-40) cc_final: 0.7942 (m-40) REVERT: E 160 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.7276 (ttm170) REVERT: R 142 TRP cc_start: 0.6883 (m-90) cc_final: 0.5798 (m100) REVERT: R 252 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.5868 (mpp-170) REVERT: R 345 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6985 (mm-40) outliers start: 31 outliers final: 15 residues processed: 159 average time/residue: 0.6723 time to fit residues: 112.8830 Evaluate side-chains 161 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN E 82 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.169001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130677 restraints weight = 8874.805| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.71 r_work: 0.3052 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9162 Z= 0.122 Angle : 0.486 5.353 12435 Z= 0.264 Chirality : 0.041 0.136 1426 Planarity : 0.004 0.057 1570 Dihedral : 5.176 59.717 1267 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.41 % Allowed : 10.32 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.49 (0.25), residues: 1144 helix: 2.63 (0.25), residues: 393 sheet: 0.27 (0.29), residues: 280 loop : 0.10 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.012 0.001 TYR E 190 PHE 0.013 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9158) covalent geometry : angle 0.48619 (12427) SS BOND : bond 0.00223 ( 4) SS BOND : angle 0.59584 ( 8) hydrogen bonds : bond 0.04312 ( 472) hydrogen bonds : angle 4.56336 ( 1329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8349 (mt-10) REVERT: A 17 LYS cc_start: 0.8365 (mttt) cc_final: 0.7975 (mtpt) REVERT: A 28 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: A 29 LYS cc_start: 0.8101 (tttt) cc_final: 0.7597 (ttpp) REVERT: A 33 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: B 217 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8340 (pmm) REVERT: C 58 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: E 43 LYS cc_start: 0.8612 (mmtm) cc_final: 0.7802 (mtmt) REVERT: E 77 ASN cc_start: 0.8366 (m-40) cc_final: 0.7967 (m-40) REVERT: E 160 ARG cc_start: 0.7544 (mtp-110) cc_final: 0.6779 (mmm160) REVERT: R 142 TRP cc_start: 0.6933 (m-90) cc_final: 0.5703 (m100) REVERT: R 187 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7054 (mm) REVERT: R 252 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6831 (mpt90) REVERT: R 356 LEU cc_start: 0.7951 (mm) cc_final: 0.7676 (mm) outliers start: 33 outliers final: 18 residues processed: 160 average time/residue: 0.6899 time to fit residues: 116.5817 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 252 ARG Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN B 259 GLN R 345 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128152 restraints weight = 8753.367| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.74 r_work: 0.2988 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9162 Z= 0.207 Angle : 0.575 7.449 12435 Z= 0.309 Chirality : 0.045 0.217 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.566 59.391 1267 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.82 % Allowed : 10.22 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.23 (0.25), residues: 1144 helix: 2.40 (0.25), residues: 394 sheet: 0.21 (0.28), residues: 297 loop : -0.11 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 224 TYR 0.014 0.002 TYR R 341 PHE 0.017 0.002 PHE B 151 TRP 0.014 0.002 TRP B 99 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9158) covalent geometry : angle 0.57433 (12427) SS BOND : bond 0.00410 ( 4) SS BOND : angle 0.92549 ( 8) hydrogen bonds : bond 0.05047 ( 472) hydrogen bonds : angle 4.81905 ( 1329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.373 Fit side-chains REVERT: A 28 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: A 29 LYS cc_start: 0.8155 (tttt) cc_final: 0.7644 (ttpp) REVERT: A 33 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: B 42 ARG cc_start: 0.6976 (tpt170) cc_final: 0.6224 (tpt170) REVERT: B 217 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8397 (pmm) REVERT: C 58 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: E 43 LYS cc_start: 0.8638 (mmtm) cc_final: 0.7817 (mtmt) REVERT: E 65 LYS cc_start: 0.8003 (tttt) cc_final: 0.7590 (ttmm) REVERT: E 160 ARG cc_start: 0.7581 (mtp-110) cc_final: 0.6801 (mmm160) REVERT: R 142 TRP cc_start: 0.6927 (m-90) cc_final: 0.5623 (m100) REVERT: R 165 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7887 (ttt) REVERT: R 250 TYR cc_start: 0.8233 (m-80) cc_final: 0.7916 (m-10) outliers start: 37 outliers final: 19 residues processed: 164 average time/residue: 0.7257 time to fit residues: 125.5155 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129224 restraints weight = 8833.265| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.66 r_work: 0.3013 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9162 Z= 0.137 Angle : 0.507 5.951 12435 Z= 0.274 Chirality : 0.042 0.136 1426 Planarity : 0.004 0.059 1570 Dihedral : 4.980 43.840 1262 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.02 % Allowed : 10.94 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.33 (0.25), residues: 1144 helix: 2.56 (0.25), residues: 394 sheet: 0.14 (0.29), residues: 283 loop : -0.03 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.012 0.001 TYR R 341 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9158) covalent geometry : angle 0.50518 (12427) SS BOND : bond 0.00261 ( 4) SS BOND : angle 1.56020 ( 8) hydrogen bonds : bond 0.04350 ( 472) hydrogen bonds : angle 4.59968 ( 1329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.370 Fit side-chains REVERT: A 28 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: A 29 LYS cc_start: 0.8125 (tttt) cc_final: 0.7628 (ttpp) REVERT: A 33 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: A 270 LYS cc_start: 0.8473 (mttt) cc_final: 0.8028 (mttp) REVERT: B 42 ARG cc_start: 0.7036 (tpt170) cc_final: 0.6288 (tpt170) REVERT: C 58 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: E 43 LYS cc_start: 0.8649 (mmtm) cc_final: 0.7894 (mtmt) REVERT: E 77 ASN cc_start: 0.8603 (m-40) cc_final: 0.8050 (m-40) REVERT: E 160 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.6783 (mmm160) REVERT: R 142 TRP cc_start: 0.6914 (m-90) cc_final: 0.5638 (m100) REVERT: R 250 TYR cc_start: 0.8172 (m-80) cc_final: 0.7882 (m-10) REVERT: R 345 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6908 (mm-40) outliers start: 39 outliers final: 21 residues processed: 164 average time/residue: 0.7356 time to fit residues: 127.1885 Evaluate side-chains 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 0.0010 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.166652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129065 restraints weight = 8742.829| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.65 r_work: 0.3103 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9162 Z= 0.177 Angle : 0.551 7.640 12435 Z= 0.295 Chirality : 0.044 0.221 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.097 43.736 1262 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.82 % Allowed : 11.25 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 (0.25), residues: 1144 helix: 2.48 (0.25), residues: 394 sheet: 0.13 (0.28), residues: 297 loop : -0.10 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 208 TYR 0.013 0.002 TYR R 341 PHE 0.015 0.002 PHE B 151 TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9158) covalent geometry : angle 0.55007 (12427) SS BOND : bond 0.00344 ( 4) SS BOND : angle 1.54422 ( 8) hydrogen bonds : bond 0.04671 ( 472) hydrogen bonds : angle 4.69905 ( 1329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.354 Fit side-chains REVERT: A 8 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8447 (mt-10) REVERT: A 28 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: A 29 LYS cc_start: 0.8201 (tttt) cc_final: 0.7732 (ttpp) REVERT: A 33 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: A 243 MET cc_start: 0.8555 (tpp) cc_final: 0.8300 (ttm) REVERT: A 270 LYS cc_start: 0.8519 (mttt) cc_final: 0.8084 (mttp) REVERT: B 42 ARG cc_start: 0.7005 (tpt170) cc_final: 0.6315 (tpt170) REVERT: C 58 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: E 43 LYS cc_start: 0.8623 (mmtm) cc_final: 0.7894 (mtmt) REVERT: E 65 LYS cc_start: 0.8007 (tttt) cc_final: 0.7650 (ttmm) REVERT: E 160 ARG cc_start: 0.7528 (mtp-110) cc_final: 0.6854 (mmm160) REVERT: R 142 TRP cc_start: 0.6956 (m-90) cc_final: 0.5714 (m100) REVERT: R 165 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7907 (ttt) outliers start: 37 outliers final: 24 residues processed: 158 average time/residue: 0.7524 time to fit residues: 125.1048 Evaluate side-chains 168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 chunk 58 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.168364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130439 restraints weight = 8784.084| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.74 r_work: 0.3131 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9162 Z= 0.126 Angle : 0.501 6.512 12435 Z= 0.269 Chirality : 0.042 0.147 1426 Planarity : 0.004 0.060 1570 Dihedral : 4.927 43.636 1262 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.30 % Allowed : 11.76 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.37 (0.25), residues: 1144 helix: 2.64 (0.26), residues: 394 sheet: 0.13 (0.29), residues: 277 loop : -0.04 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 208 TYR 0.011 0.001 TYR R 341 PHE 0.013 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9158) covalent geometry : angle 0.50041 (12427) SS BOND : bond 0.00230 ( 4) SS BOND : angle 1.21929 ( 8) hydrogen bonds : bond 0.04162 ( 472) hydrogen bonds : angle 4.54042 ( 1329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.357 Fit side-chains REVERT: A 28 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7374 (mt-10) REVERT: A 29 LYS cc_start: 0.8167 (tttt) cc_final: 0.7680 (ttpp) REVERT: A 32 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7743 (mtt90) REVERT: A 33 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7771 (mt-10) REVERT: A 270 LYS cc_start: 0.8518 (mttt) cc_final: 0.8074 (mttp) REVERT: B 42 ARG cc_start: 0.7056 (tpt170) cc_final: 0.6364 (tpt170) REVERT: C 58 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: E 43 LYS cc_start: 0.8632 (mmtm) cc_final: 0.7864 (mtpt) REVERT: E 77 ASN cc_start: 0.8609 (m-40) cc_final: 0.8092 (m-40) REVERT: E 160 ARG cc_start: 0.7478 (mtp-110) cc_final: 0.7219 (ttm170) REVERT: R 142 TRP cc_start: 0.6970 (m-90) cc_final: 0.5724 (m100) REVERT: R 165 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7981 (ttt) REVERT: R 184 MET cc_start: 0.7137 (tpt) cc_final: 0.6889 (tpt) REVERT: R 250 TYR cc_start: 0.8234 (m-80) cc_final: 0.7945 (m-10) outliers start: 32 outliers final: 20 residues processed: 158 average time/residue: 0.7586 time to fit residues: 126.2051 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.167059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129096 restraints weight = 8669.090| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.72 r_work: 0.3006 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9162 Z= 0.163 Angle : 0.545 7.403 12435 Z= 0.291 Chirality : 0.044 0.200 1426 Planarity : 0.004 0.060 1570 Dihedral : 5.065 43.615 1262 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.20 % Allowed : 11.66 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.30 (0.25), residues: 1144 helix: 2.58 (0.25), residues: 394 sheet: 0.11 (0.28), residues: 297 loop : -0.08 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.013 0.002 TYR R 341 PHE 0.014 0.002 PHE B 151 TRP 0.013 0.002 TRP B 99 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9158) covalent geometry : angle 0.54402 (12427) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.33490 ( 8) hydrogen bonds : bond 0.04519 ( 472) hydrogen bonds : angle 4.65909 ( 1329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.395 Fit side-chains REVERT: A 8 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8369 (mt-10) REVERT: A 28 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: A 29 LYS cc_start: 0.8099 (tttt) cc_final: 0.7583 (ttpp) REVERT: A 33 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: A 270 LYS cc_start: 0.8489 (mttt) cc_final: 0.8023 (mttp) REVERT: B 42 ARG cc_start: 0.7099 (tpt170) cc_final: 0.6361 (tpt170) REVERT: C 58 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: E 43 LYS cc_start: 0.8612 (mmtm) cc_final: 0.7768 (mtpt) REVERT: E 160 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7285 (ttm170) REVERT: R 142 TRP cc_start: 0.6891 (m-90) cc_final: 0.5609 (m100) REVERT: R 165 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7899 (ttt) REVERT: R 250 TYR cc_start: 0.8158 (m-80) cc_final: 0.7868 (m-10) REVERT: R 345 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6854 (mm110) outliers start: 31 outliers final: 21 residues processed: 152 average time/residue: 0.7858 time to fit residues: 125.5675 Evaluate side-chains 164 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.168407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130533 restraints weight = 8710.962| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.73 r_work: 0.3034 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9162 Z= 0.126 Angle : 0.511 7.318 12435 Z= 0.274 Chirality : 0.042 0.144 1426 Planarity : 0.004 0.060 1570 Dihedral : 4.964 44.038 1262 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.89 % Allowed : 12.07 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.35 (0.25), residues: 1144 helix: 2.64 (0.25), residues: 396 sheet: 0.09 (0.29), residues: 278 loop : -0.04 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 208 TYR 0.012 0.001 TYR R 341 PHE 0.012 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9158) covalent geometry : angle 0.51047 (12427) SS BOND : bond 0.00198 ( 4) SS BOND : angle 1.23612 ( 8) hydrogen bonds : bond 0.04163 ( 472) hydrogen bonds : angle 4.56685 ( 1329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.382 Fit side-chains REVERT: A 8 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 28 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: A 29 LYS cc_start: 0.8071 (tttt) cc_final: 0.7566 (ttpp) REVERT: A 33 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: A 270 LYS cc_start: 0.8493 (mttt) cc_final: 0.8026 (mttp) REVERT: B 42 ARG cc_start: 0.7081 (tpt170) cc_final: 0.6343 (tpt170) REVERT: B 219 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8257 (mmt180) REVERT: C 58 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: E 43 LYS cc_start: 0.8613 (mmtm) cc_final: 0.7791 (mtpt) REVERT: E 77 ASN cc_start: 0.8584 (m-40) cc_final: 0.8086 (m-40) REVERT: E 160 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7231 (ttm170) REVERT: R 142 TRP cc_start: 0.6901 (m-90) cc_final: 0.5650 (m100) REVERT: R 165 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7924 (ttt) REVERT: R 345 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6883 (mm110) outliers start: 28 outliers final: 20 residues processed: 158 average time/residue: 0.7497 time to fit residues: 124.7316 Evaluate side-chains 167 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 230 THR Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 345 GLN Chi-restraints excluded: chain L residue 14 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 0.0030 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 156 GLN R 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.168981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131687 restraints weight = 8695.006| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.63 r_work: 0.3150 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9162 Z= 0.124 Angle : 0.517 7.400 12435 Z= 0.276 Chirality : 0.042 0.193 1426 Planarity : 0.004 0.060 1570 Dihedral : 4.920 43.461 1262 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.68 % Allowed : 12.59 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.38 (0.25), residues: 1144 helix: 2.68 (0.26), residues: 396 sheet: 0.07 (0.29), residues: 278 loop : -0.03 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.011 0.001 TYR E 190 PHE 0.014 0.001 PHE R 283 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9158) covalent geometry : angle 0.51578 (12427) SS BOND : bond 0.00184 ( 4) SS BOND : angle 1.73209 ( 8) hydrogen bonds : bond 0.04096 ( 472) hydrogen bonds : angle 4.65166 ( 1329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4218.16 seconds wall clock time: 72 minutes 38.43 seconds (4358.43 seconds total)