Starting phenix.real_space_refine on Sat Jun 14 15:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bip_44597/06_2025/9bip_44597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bip_44597/06_2025/9bip_44597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bip_44597/06_2025/9bip_44597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bip_44597/06_2025/9bip_44597.map" model { file = "/net/cci-nas-00/data/ceres_data/9bip_44597/06_2025/9bip_44597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bip_44597/06_2025/9bip_44597.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.161 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5265 2.51 5 N 1466 2.21 5 O 1542 1.98 5 H 8135 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16460 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3954 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 5059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5059 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 867 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1900 Classifications: {'peptide': 128} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 4680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 4680 Classifications: {'peptide': 290} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277} Time building chain proxies: 7.65, per 1000 atoms: 0.46 Number of scatterers: 16460 At special positions: 0 Unit cell: (75.68, 104.06, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1542 8.00 N 1466 7.00 C 5265 6.00 H 8135 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 3.64 Conformation dependent library (CDL) restraints added in 1.2 seconds 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.528A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.740A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 252 through 264 No H-bonds generated for 'chain 'A' and resid 252 through 264' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.581A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.577A pdb=" N ASP A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.672A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.506A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.857A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.763A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.689A pdb=" N SER R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL R 30 " --> pdb=" O PHE R 26 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 68 removed outlier: 4.183A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 79 removed outlier: 4.124A pdb=" N TRP R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 121 removed outlier: 5.377A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 150 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.676A pdb=" N PHE R 154 " --> pdb=" O ALA R 151 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 151 through 155' Processing helix chain 'R' and resid 175 through 209 removed outlier: 3.651A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE R 192 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 215 through 254 removed outlier: 3.794A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 264 removed outlier: 3.594A pdb=" N ARG R 263 " --> pdb=" O GLY R 259 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 275 removed outlier: 3.624A pdb=" N THR R 275 " --> pdb=" O SER R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 292 through 296 removed outlier: 3.838A pdb=" N ASP R 296 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.601A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.543A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.823A 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: 3.828A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.671A 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: 7.212A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.760A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.977A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.442A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.050A 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: 3.872A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.551A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.585A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA N 97 " --> pdb=" O ASN N 35 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.432A 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) Processing sheet with id=AB2, first strand: chain 'R' and resid 158 through 160 401 hydrogen bonds defined for protein. 1146 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: 5.30 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8109 1.03 - 1.23: 132 1.23 - 1.43: 3575 1.43 - 1.62: 4757 1.62 - 1.82: 70 Bond restraints: 16643 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.09e+00 bond pdb=" N ASN G 5 " pdb=" CA ASN G 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N THR A 9 " pdb=" CA THR A 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N THR A 9 " pdb=" H THR A 9 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N ASN G 5 " pdb=" H ASN G 5 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.23e+00 ... (remaining 16638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 27626 1.02 - 2.03: 2143 2.03 - 3.05: 94 3.05 - 4.06: 31 4.06 - 5.08: 7 Bond angle restraints: 29901 Sorted by residual: angle pdb=" N ALA N 92 " pdb=" CA ALA N 92 " pdb=" C ALA N 92 " ideal model delta sigma weight residual 107.73 111.33 -3.60 1.61e+00 3.86e-01 4.99e+00 angle pdb=" N ARG R 14 " pdb=" CA ARG R 14 " pdb=" C ARG R 14 " ideal model delta sigma weight residual 114.56 111.82 2.74 1.27e+00 6.20e-01 4.66e+00 angle pdb=" C GLN A 59 " pdb=" N MET A 60 " pdb=" CA MET A 60 " ideal model delta sigma weight residual 121.14 117.95 3.19 1.75e+00 3.27e-01 3.33e+00 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 112.47 116.16 -3.69 2.06e+00 2.36e-01 3.21e+00 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 110.53 108.17 2.36 1.32e+00 5.74e-01 3.21e+00 ... (remaining 29896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7014 17.88 - 35.75: 605 35.75 - 53.63: 190 53.63 - 71.51: 41 71.51 - 89.39: 14 Dihedral angle restraints: 7864 sinusoidal: 4181 harmonic: 3683 Sorted by residual: dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -126.33 40.33 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 7861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 765 0.028 - 0.055: 314 0.055 - 0.083: 105 0.083 - 0.110: 62 0.110 - 0.138: 28 Chirality restraints: 1274 Sorted by residual: chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1271 not shown) Planarity restraints: 2504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 186 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C VAL R 186 " 0.035 2.00e-02 2.50e+03 pdb=" O VAL R 186 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE R 187 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 236 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 361 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.023 5.00e-02 4.00e+02 ... (remaining 2501 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1203 2.21 - 2.81: 33078 2.81 - 3.41: 41571 3.41 - 4.00: 55986 4.00 - 4.60: 87210 Nonbonded interactions: 219048 Sorted by model distance: nonbonded pdb=" OE1 GLN N 53 " pdb=" H GLN N 53 " model vdw 1.616 2.450 nonbonded pdb="HE21 GLN N 39 " pdb=" O LYS N 43 " model vdw 1.626 2.450 nonbonded pdb=" O ASP B 163 " pdb=" HG1 THR B 164 " model vdw 1.671 2.450 nonbonded pdb=" O ARG A 283 " pdb=" HG1 THR A 284 " model vdw 1.678 2.450 nonbonded pdb=" O ASP B 333 " pdb=" HG SER B 334 " model vdw 1.683 2.450 ... (remaining 219043 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: 1.670 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: 0.280 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.820 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.003 0.039 8512 Z= 0.125 Angle : 0.513 5.079 11540 Z= 0.283 Chirality : 0.041 0.138 1274 Planarity : 0.003 0.044 1486 Dihedral : 16.505 89.385 3060 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.91 % Allowed : 18.97 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1044 helix: 2.03 (0.27), residues: 402 sheet: -0.54 (0.34), residues: 223 loop : -1.57 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 73 HIS 0.004 0.001 HIS A 220 PHE 0.010 0.001 PHE R 159 TYR 0.008 0.001 TYR N 95 ARG 0.002 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.18167 ( 401) hydrogen bonds : angle 5.75308 ( 1146) SS BOND : bond 0.00325 ( 4) SS BOND : angle 0.98697 ( 8) covalent geometry : bond 0.00253 ( 8508) covalent geometry : angle 0.51211 (11532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.351 Fit side-chains REVERT: A 27 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 64 HIS cc_start: 0.3312 (OUTLIER) cc_final: 0.2271 (t70) REVERT: A 266 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8437 (mp) REVERT: A 327 GLU cc_start: 0.4712 (OUTLIER) cc_final: 0.2372 (mp0) REVERT: B 59 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8482 (t80) REVERT: B 259 GLN cc_start: 0.7940 (tt0) cc_final: 0.7627 (mt0) REVERT: R 181 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.6501 (tmm) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 3.0885 time to fit residues: 289.5381 Evaluate side-chains 88 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 156 ASP Chi-restraints excluded: chain R residue 181 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN R 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128592 restraints weight = 26157.821| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.12 r_work: 0.3375 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8512 Z= 0.178 Angle : 0.600 6.072 11540 Z= 0.329 Chirality : 0.044 0.180 1274 Planarity : 0.004 0.048 1486 Dihedral : 7.248 58.476 1193 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.59 % Allowed : 16.95 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1044 helix: 1.79 (0.26), residues: 408 sheet: -0.47 (0.34), residues: 216 loop : -1.53 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.009 0.001 HIS R 79 PHE 0.014 0.002 PHE B 151 TYR 0.012 0.002 TYR N 95 ARG 0.004 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.07054 ( 401) hydrogen bonds : angle 4.73827 ( 1146) SS BOND : bond 0.00580 ( 4) SS BOND : angle 1.23108 ( 8) covalent geometry : bond 0.00407 ( 8508) covalent geometry : angle 0.59968 (11532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: B 59 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8513 (t80) REVERT: B 175 GLN cc_start: 0.7874 (mm110) cc_final: 0.7433 (mt0) REVERT: B 259 GLN cc_start: 0.7709 (tt0) cc_final: 0.7341 (mt0) REVERT: B 284 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8003 (mp) REVERT: N 98 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8371 (ppt90) REVERT: R 115 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8078 (mtm-85) REVERT: R 123 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7101 (mt) outliers start: 32 outliers final: 12 residues processed: 102 average time/residue: 2.9602 time to fit residues: 319.0741 Evaluate side-chains 91 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 211 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129619 restraints weight = 25910.650| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.12 r_work: 0.3366 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8512 Z= 0.152 Angle : 0.563 5.116 11540 Z= 0.309 Chirality : 0.042 0.166 1274 Planarity : 0.004 0.048 1486 Dihedral : 5.970 59.709 1170 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.93 % Allowed : 17.28 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1044 helix: 1.86 (0.26), residues: 407 sheet: -0.39 (0.34), residues: 212 loop : -1.53 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.005 0.001 HIS A 362 PHE 0.015 0.001 PHE R 19 TYR 0.014 0.002 TYR N 95 ARG 0.003 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.06425 ( 401) hydrogen bonds : angle 4.51626 ( 1146) SS BOND : bond 0.00491 ( 4) SS BOND : angle 1.21682 ( 8) covalent geometry : bond 0.00340 ( 8508) covalent geometry : angle 0.56232 (11532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: B 22 ARG cc_start: 0.5529 (mtt180) cc_final: 0.5258 (mtt90) REVERT: B 59 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8445 (t80) REVERT: B 175 GLN cc_start: 0.7834 (mm110) cc_final: 0.7424 (mt0) REVERT: B 259 GLN cc_start: 0.7668 (tt0) cc_final: 0.7328 (mt0) REVERT: B 284 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8067 (mp) REVERT: N 98 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8219 (ppt170) REVERT: R 123 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6998 (mt) outliers start: 35 outliers final: 18 residues processed: 107 average time/residue: 2.6538 time to fit residues: 301.9896 Evaluate side-chains 97 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.171356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131286 restraints weight = 26364.814| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.15 r_work: 0.3424 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8512 Z= 0.128 Angle : 0.531 5.010 11540 Z= 0.290 Chirality : 0.041 0.153 1274 Planarity : 0.004 0.047 1486 Dihedral : 5.759 59.212 1169 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.93 % Allowed : 17.28 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1044 helix: 2.02 (0.27), residues: 407 sheet: -0.38 (0.34), residues: 212 loop : -1.51 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS R 79 PHE 0.017 0.001 PHE R 19 TYR 0.014 0.001 TYR N 95 ARG 0.002 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.05778 ( 401) hydrogen bonds : angle 4.37287 ( 1146) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.10076 ( 8) covalent geometry : bond 0.00276 ( 8508) covalent geometry : angle 0.53034 (11532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 79 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8336 (mp) REVERT: A 309 GLU cc_start: 0.5565 (pm20) cc_final: 0.5322 (pp20) REVERT: A 327 GLU cc_start: 0.4549 (OUTLIER) cc_final: 0.2913 (mp0) REVERT: A 344 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.6889 (mt-10) REVERT: B 22 ARG cc_start: 0.5545 (mtt180) cc_final: 0.5290 (mtt90) REVERT: B 59 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 175 GLN cc_start: 0.7767 (mm110) cc_final: 0.7345 (mt0) REVERT: B 259 GLN cc_start: 0.7625 (tt0) cc_final: 0.7313 (mt0) REVERT: B 284 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8039 (mp) REVERT: B 318 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8734 (tt) REVERT: N 98 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8236 (ppt170) REVERT: R 115 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7766 (mtt180) REVERT: R 123 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6925 (mt) outliers start: 35 outliers final: 19 residues processed: 109 average time/residue: 2.7320 time to fit residues: 315.8720 Evaluate side-chains 104 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 19 optimal weight: 0.0060 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133171 restraints weight = 26526.693| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.04 r_work: 0.3439 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8512 Z= 0.105 Angle : 0.490 5.024 11540 Z= 0.267 Chirality : 0.040 0.139 1274 Planarity : 0.003 0.047 1486 Dihedral : 5.476 58.219 1169 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.25 % Allowed : 17.85 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1044 helix: 2.24 (0.27), residues: 407 sheet: -0.33 (0.34), residues: 220 loop : -1.43 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.004 0.001 HIS R 79 PHE 0.010 0.001 PHE R 97 TYR 0.012 0.001 TYR N 95 ARG 0.002 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.04966 ( 401) hydrogen bonds : angle 4.19136 ( 1146) SS BOND : bond 0.00329 ( 4) SS BOND : angle 0.96778 ( 8) covalent geometry : bond 0.00219 ( 8508) covalent geometry : angle 0.48958 (11532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7641 (m-30) cc_final: 0.7316 (p0) REVERT: A 266 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8381 (mp) REVERT: A 327 GLU cc_start: 0.4612 (OUTLIER) cc_final: 0.4343 (mt-10) REVERT: B 22 ARG cc_start: 0.5587 (mtt180) cc_final: 0.5359 (mtt90) REVERT: B 59 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8388 (t80) REVERT: B 175 GLN cc_start: 0.7810 (mm110) cc_final: 0.7388 (mt0) REVERT: B 259 GLN cc_start: 0.7687 (tt0) cc_final: 0.7361 (mt0) REVERT: B 318 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8652 (tt) REVERT: N 98 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8437 (ppt90) REVERT: R 115 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7779 (mtt180) REVERT: R 123 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6827 (mt) outliers start: 29 outliers final: 17 residues processed: 103 average time/residue: 2.9272 time to fit residues: 319.3700 Evaluate side-chains 99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133084 restraints weight = 26262.401| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.16 r_work: 0.3442 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8512 Z= 0.114 Angle : 0.502 4.912 11540 Z= 0.273 Chirality : 0.041 0.141 1274 Planarity : 0.004 0.050 1486 Dihedral : 5.481 58.129 1169 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.70 % Allowed : 17.40 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1044 helix: 2.27 (0.27), residues: 407 sheet: -0.27 (0.35), residues: 209 loop : -1.44 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 PHE 0.010 0.001 PHE B 151 TYR 0.013 0.001 TYR N 95 ARG 0.009 0.000 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 401) hydrogen bonds : angle 4.17293 ( 1146) SS BOND : bond 0.00371 ( 4) SS BOND : angle 1.01693 ( 8) covalent geometry : bond 0.00245 ( 8508) covalent geometry : angle 0.50096 (11532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.6414 (mp0) REVERT: A 266 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8357 (mp) REVERT: A 327 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.4295 (mt-10) REVERT: A 344 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: B 22 ARG cc_start: 0.5511 (mtt180) cc_final: 0.5293 (mtt90) REVERT: B 59 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8374 (t80) REVERT: B 175 GLN cc_start: 0.7796 (mm110) cc_final: 0.7323 (mt0) REVERT: B 259 GLN cc_start: 0.7663 (tt0) cc_final: 0.7321 (mt0) REVERT: B 318 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8664 (tt) REVERT: N 98 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8430 (ppt90) REVERT: R 115 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7873 (mtt180) REVERT: R 123 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6797 (mt) outliers start: 33 outliers final: 16 residues processed: 105 average time/residue: 2.9357 time to fit residues: 326.3116 Evaluate side-chains 99 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128418 restraints weight = 26390.036| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.96 r_work: 0.3382 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8512 Z= 0.157 Angle : 0.562 5.441 11540 Z= 0.307 Chirality : 0.043 0.178 1274 Planarity : 0.004 0.060 1486 Dihedral : 5.785 58.051 1169 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.15 % Allowed : 17.40 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1044 helix: 2.07 (0.26), residues: 408 sheet: -0.28 (0.35), residues: 211 loop : -1.49 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.013 0.001 PHE B 151 TYR 0.017 0.002 TYR N 95 ARG 0.009 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.06222 ( 401) hydrogen bonds : angle 4.35255 ( 1146) SS BOND : bond 0.00444 ( 4) SS BOND : angle 1.42988 ( 8) covalent geometry : bond 0.00358 ( 8508) covalent geometry : angle 0.56048 (11532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8411 (mp) REVERT: A 309 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.4915 (pp20) REVERT: A 327 GLU cc_start: 0.4628 (OUTLIER) cc_final: 0.3017 (mp0) REVERT: A 344 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7773 (mm-30) REVERT: B 22 ARG cc_start: 0.5757 (mtt180) cc_final: 0.5540 (mtt90) REVERT: B 59 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8511 (t80) REVERT: B 175 GLN cc_start: 0.7949 (mm110) cc_final: 0.7522 (mt0) REVERT: B 259 GLN cc_start: 0.7792 (tt0) cc_final: 0.7473 (mt0) REVERT: B 284 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 318 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8817 (tt) REVERT: N 98 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8332 (ppt170) REVERT: R 115 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7735 (mtt180) REVERT: R 123 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7065 (mt) outliers start: 37 outliers final: 19 residues processed: 108 average time/residue: 2.7506 time to fit residues: 314.7967 Evaluate side-chains 103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128820 restraints weight = 26116.546| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.95 r_work: 0.3367 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8512 Z= 0.149 Angle : 0.553 5.161 11540 Z= 0.302 Chirality : 0.042 0.171 1274 Planarity : 0.004 0.069 1486 Dihedral : 5.803 57.016 1169 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.15 % Allowed : 17.51 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1044 helix: 2.04 (0.26), residues: 408 sheet: -0.30 (0.34), residues: 211 loop : -1.50 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.023 0.001 PHE R 19 TYR 0.014 0.002 TYR N 95 ARG 0.010 0.000 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.06084 ( 401) hydrogen bonds : angle 4.33766 ( 1146) SS BOND : bond 0.00370 ( 4) SS BOND : angle 1.67155 ( 8) covalent geometry : bond 0.00336 ( 8508) covalent geometry : angle 0.55164 (11532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 75 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7961 (m-30) cc_final: 0.7723 (m-30) REVERT: A 266 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 309 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.4940 (pp20) REVERT: A 327 GLU cc_start: 0.4566 (OUTLIER) cc_final: 0.3087 (mp0) REVERT: A 344 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7094 (mt-10) REVERT: B 22 ARG cc_start: 0.5732 (mtt180) cc_final: 0.5517 (mtt90) REVERT: B 59 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8545 (t80) REVERT: B 175 GLN cc_start: 0.7986 (mm110) cc_final: 0.7557 (mt0) REVERT: B 259 GLN cc_start: 0.7790 (tt0) cc_final: 0.7519 (mt0) REVERT: B 284 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7999 (mp) REVERT: B 318 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8813 (tt) REVERT: N 98 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8287 (ppt170) REVERT: R 115 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7886 (mtt180) REVERT: R 123 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7093 (mt) outliers start: 37 outliers final: 23 residues processed: 108 average time/residue: 2.5819 time to fit residues: 297.3203 Evaluate side-chains 105 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 72 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 246 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 86 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128864 restraints weight = 26291.471| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.95 r_work: 0.3368 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8512 Z= 0.143 Angle : 0.546 5.062 11540 Z= 0.299 Chirality : 0.042 0.165 1274 Planarity : 0.004 0.046 1486 Dihedral : 5.771 57.119 1169 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.15 % Allowed : 17.62 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1044 helix: 2.06 (0.26), residues: 407 sheet: -0.23 (0.34), residues: 209 loop : -1.51 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.012 0.001 PHE B 151 TYR 0.014 0.001 TYR N 95 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05973 ( 401) hydrogen bonds : angle 4.32049 ( 1146) SS BOND : bond 0.00378 ( 4) SS BOND : angle 1.49718 ( 8) covalent geometry : bond 0.00320 ( 8508) covalent geometry : angle 0.54505 (11532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.7994 (m-30) cc_final: 0.7750 (m-30) REVERT: A 266 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8454 (mp) REVERT: A 309 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4931 (pp20) REVERT: A 327 GLU cc_start: 0.4609 (OUTLIER) cc_final: 0.3139 (mp0) REVERT: A 344 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7117 (mt-10) REVERT: B 59 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8540 (t80) REVERT: B 175 GLN cc_start: 0.8025 (mm110) cc_final: 0.7590 (mt0) REVERT: B 259 GLN cc_start: 0.7802 (tt0) cc_final: 0.7524 (mt0) REVERT: B 284 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8056 (mp) REVERT: B 318 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8803 (tt) REVERT: N 98 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8300 (ppt170) REVERT: R 115 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7773 (mtt180) REVERT: R 123 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7069 (mt) outliers start: 37 outliers final: 23 residues processed: 104 average time/residue: 2.3914 time to fit residues: 266.1467 Evaluate side-chains 103 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 246 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.130253 restraints weight = 26336.979| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.96 r_work: 0.3390 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8512 Z= 0.121 Angle : 0.517 5.001 11540 Z= 0.282 Chirality : 0.041 0.144 1274 Planarity : 0.004 0.047 1486 Dihedral : 5.604 56.894 1169 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.70 % Allowed : 18.18 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1044 helix: 2.19 (0.27), residues: 407 sheet: -0.24 (0.34), residues: 210 loop : -1.49 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 362 PHE 0.010 0.001 PHE R 159 TYR 0.013 0.001 TYR N 95 ARG 0.007 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05403 ( 401) hydrogen bonds : angle 4.23242 ( 1146) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.40192 ( 8) covalent geometry : bond 0.00262 ( 8508) covalent geometry : angle 0.51584 (11532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2088 Ramachandran restraints generated. 1044 Oldfield, 0 Emsley, 1044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 46 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7095 (mt-10) REVERT: B 22 ARG cc_start: 0.5731 (mtt180) cc_final: 0.5528 (mtt90) REVERT: B 59 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8503 (t80) REVERT: B 175 GLN cc_start: 0.7987 (mm110) cc_final: 0.7520 (mt0) REVERT: B 259 GLN cc_start: 0.7767 (tt0) cc_final: 0.7457 (mt0) REVERT: B 284 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8040 (mp) REVERT: B 318 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8727 (tt) REVERT: N 98 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8299 (ppt170) REVERT: R 115 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7972 (mtt180) REVERT: R 123 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6957 (mt) outliers start: 33 outliers final: 19 residues processed: 104 average time/residue: 2.6301 time to fit residues: 291.3906 Evaluate side-chains 101 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 98 ARG Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 115 ARG Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain R residue 211 SER Chi-restraints excluded: chain R residue 246 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.133197 restraints weight = 26334.706| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.16 r_work: 0.3436 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8512 Z= 0.106 Angle : 0.494 4.981 11540 Z= 0.268 Chirality : 0.040 0.140 1274 Planarity : 0.004 0.047 1486 Dihedral : 5.403 56.496 1169 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.03 % Allowed : 18.86 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1044 helix: 2.33 (0.27), residues: 407 sheet: -0.12 (0.35), residues: 204 loop : -1.45 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 362 PHE 0.010 0.001 PHE R 159 TYR 0.012 0.001 TYR N 95 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 401) hydrogen bonds : angle 4.13541 ( 1146) SS BOND : bond 0.00241 ( 4) SS BOND : angle 1.29379 ( 8) covalent geometry : bond 0.00226 ( 8508) covalent geometry : angle 0.49267 (11532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11437.46 seconds wall clock time: 194 minutes 20.19 seconds (11660.19 seconds total)