Starting phenix.real_space_refine on Wed Aug 5 05:15:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vuq_43536/08_2026/8vuq_43536.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vuq_43536/08_2026/8vuq_43536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vuq_43536/08_2026/8vuq_43536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vuq_43536/08_2026/8vuq_43536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vuq_43536/08_2026/8vuq_43536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vuq_43536/08_2026/8vuq_43536.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5500 2.51 5 N 1492 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2789 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 17, 'TRANS': 351} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 11, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2697 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 15, 'TRANS': 347} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 10, 'GLU:plan': 12, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "G" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1617 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1554 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.01, per 1000 atoms: 0.23 Number of scatterers: 8657 At special positions: 0 Unit cell: (107, 113.848, 124.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1629 8.00 N 1492 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 149 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 493.2 milliseconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 19 sheets defined 24.9% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.570A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.937A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.554A pdb=" N PHE A 102 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.506A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.797A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.518A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.659A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.502A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.757A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.832A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 107 through 119 removed outlier: 4.095A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.613A pdb=" N SER B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 129 through 133' Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.933A pdb=" N PHE B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 4.312A pdb=" N GLN B 216 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.675A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.672A pdb=" N ARG B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.872A pdb=" N VAL B 339 " --> pdb=" O PRO B 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 196 through 198 No H-bonds generated for 'chain 'G' and resid 196 through 198' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.768A pdb=" N ASN I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 removed outlier: 3.751A pdb=" N ALA I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 removed outlier: 3.749A pdb=" N HIS I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.502A pdb=" N LEU A 33 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.734A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.731A pdb=" N VAL A 167 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 340 through 341 removed outlier: 3.734A pdb=" N ASN A 341 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 344 " --> pdb=" O ASN A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 72 removed outlier: 7.047A pdb=" N ALA B 37 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.878A pdb=" N PHE B 170 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N VAL B 279 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 364 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.572A pdb=" N VAL B 341 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 348 " --> pdb=" O VAL B 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.857A pdb=" N LEU G 81 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 60 removed outlier: 3.551A pdb=" N GLY G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA G 97 " --> pdb=" O HIS G 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G 190 " --> pdb=" O HIS G 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 129 through 133 removed outlier: 4.285A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL G 193 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 147 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR G 185 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER G 186 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 159 through 163 Processing sheet with id=AB6, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.762A pdb=" N VAL I 10 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN I 39 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR I 90 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 18 through 20 removed outlier: 4.072A pdb=" N VAL I 18 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE I 78 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 66 " --> pdb=" O SER I 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 114 through 118 removed outlier: 6.057A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA I 173 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 154 through 155 removed outlier: 4.065A pdb=" N TRP I 148 " --> pdb=" O VAL I 155 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS I 149 " --> pdb=" O SER I 192 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER I 192 " --> pdb=" O LYS I 149 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2801 1.34 - 1.46: 2083 1.46 - 1.58: 3917 1.58 - 1.70: 2 1.70 - 1.82: 60 Bond restraints: 8863 Sorted by residual: bond pdb=" CB PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 1.506 1.587 -0.081 3.90e-02 6.57e+02 4.28e+00 bond pdb=" N PRO G 156 " pdb=" CA PRO G 156 " ideal model delta sigma weight residual 1.468 1.435 0.033 1.70e-02 3.46e+03 3.80e+00 bond pdb=" CG PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.18e+00 bond pdb=" CB PRO A 304 " pdb=" CG PRO A 304 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CA ASN I 53 " pdb=" CB ASN I 53 " ideal model delta sigma weight residual 1.539 1.598 -0.058 4.88e-02 4.20e+02 1.43e+00 ... (remaining 8858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 12010 2.82 - 5.64: 74 5.64 - 8.47: 8 8.47 - 11.29: 1 11.29 - 14.11: 1 Bond angle restraints: 12094 Sorted by residual: angle pdb=" CA PRO G 156 " pdb=" N PRO G 156 " pdb=" CD PRO G 156 " ideal model delta sigma weight residual 111.50 97.39 14.11 1.40e+00 5.10e-01 1.02e+02 angle pdb=" C THR I 83 " pdb=" CA THR I 83 " pdb=" CB THR I 83 " ideal model delta sigma weight residual 116.54 110.04 6.50 1.15e+00 7.56e-01 3.19e+01 angle pdb=" N PRO G 156 " pdb=" CD PRO G 156 " pdb=" CG PRO G 156 " ideal model delta sigma weight residual 103.80 98.76 5.04 1.20e+00 6.94e-01 1.76e+01 angle pdb=" CA THR I 83 " pdb=" C THR I 83 " pdb=" N GLU I 84 " ideal model delta sigma weight residual 119.52 116.77 2.75 7.90e-01 1.60e+00 1.21e+01 angle pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" CD PRO A 304 " ideal model delta sigma weight residual 112.00 107.37 4.63 1.40e+00 5.10e-01 1.09e+01 ... (remaining 12089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4498 17.96 - 35.91: 566 35.91 - 53.87: 147 53.87 - 71.82: 24 71.82 - 89.78: 12 Dihedral angle restraints: 5247 sinusoidal: 1891 harmonic: 3356 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " ideal model delta harmonic sigma weight residual 180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PRO A 142 " pdb=" C PRO A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP I 138 " pdb=" CB ASP I 138 " pdb=" CG ASP I 138 " pdb=" OD1 ASP I 138 " ideal model delta sinusoidal sigma weight residual -30.00 -88.25 58.25 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 802 0.029 - 0.058: 393 0.058 - 0.087: 105 0.087 - 0.117: 82 0.117 - 0.146: 15 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB THR G 91 " pdb=" CA THR G 91 " pdb=" OG1 THR G 91 " pdb=" CG2 THR G 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 227 " pdb=" N ILE B 227 " pdb=" C ILE B 227 " pdb=" CB ILE B 227 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA VAL G 40 " pdb=" N VAL G 40 " pdb=" C VAL G 40 " pdb=" CB VAL G 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1394 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 155 " -0.089 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO G 156 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO G 156 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO G 156 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " -0.045 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 304 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 318 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO A 319 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 319 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 319 " -0.026 5.00e-02 4.00e+02 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 245 2.69 - 3.24: 8282 3.24 - 3.79: 12495 3.79 - 4.35: 15199 4.35 - 4.90: 26229 Nonbonded interactions: 62450 Sorted by model distance: nonbonded pdb=" O ASN I 53 " pdb=" ND2 ASN I 53 " model vdw 2.133 3.120 nonbonded pdb=" O MET I 3 " pdb=" OG SER I 25 " model vdw 2.146 3.040 nonbonded pdb=" O PHE B 195 " pdb=" N GLY B 197 " model vdw 2.163 3.120 nonbonded pdb=" OG SER A 93 " pdb=" OE2 GLU A 277 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN B 154 " pdb=" OG SER B 259 " model vdw 2.216 3.040 ... (remaining 62445 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 group one per residue 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: 8.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 0.081 8869 Z= 0.121 Angle : 0.615 14.112 12106 Z= 0.328 Chirality : 0.042 0.146 1397 Planarity : 0.005 0.124 1541 Dihedral : 17.334 89.781 3071 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.06 % Favored : 87.51 % Rotamer: Outliers : 0.66 % Allowed : 35.83 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.26), residues: 1153 helix: 0.75 (0.37), residues: 218 sheet: -1.03 (0.32), residues: 317 loop : -1.89 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 87 TYR 0.021 0.001 TYR B 321 PHE 0.009 0.001 PHE B 210 TRP 0.022 0.001 TRP B 284 HIS 0.005 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 8863) covalent geometry : angle 0.61563 / 0.33 (12094) SS BOND : bond 0.00254 / 0.20 ( 6) SS BOND : angle 0.37306 / 0.25 ( 12) hydrogen bonds : bond 0.27234 / 18.20 ( 251) hydrogen bonds : angle 8.89198 / 6.29 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.339 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 132 average time/residue: 0.0937 time to fit residues: 17.4091 Evaluate side-chains 127 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 338 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112957 restraints weight = 15846.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110770 restraints weight = 16632.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111660 restraints weight = 18279.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113760 restraints weight = 11778.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113884 restraints weight = 8563.412| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8869 Z= 0.141 Angle : 0.599 8.009 12106 Z= 0.313 Chirality : 0.043 0.137 1397 Planarity : 0.004 0.080 1541 Dihedral : 4.196 22.300 1244 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.40 % Favored : 87.16 % Rotamer: Outliers : 6.17 % Allowed : 28.45 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.26), residues: 1153 helix: 0.80 (0.35), residues: 247 sheet: -0.84 (0.32), residues: 317 loop : -2.11 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.012 0.001 TYR B 321 PHE 0.013 0.001 PHE B 210 TRP 0.013 0.001 TRP B 284 HIS 0.003 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 8863) covalent geometry : angle 0.59892 / 0.31 (12094) SS BOND : bond 0.00369 / 0.27 ( 6) SS BOND : angle 0.87812 / 0.57 ( 12) hydrogen bonds : bond 0.05173 / 3.60 ( 251) hydrogen bonds : angle 6.01518 / 4.24 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 140 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8171 (ptm160) REVERT: A 162 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6836 (m90) REVERT: A 295 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8929 (tp) REVERT: A 392 TYR cc_start: 0.6838 (m-10) cc_final: 0.6238 (m-10) REVERT: B 348 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8849 (pp) REVERT: B 378 TRP cc_start: 0.8400 (OUTLIER) cc_final: 0.7820 (t60) REVERT: G 49 SER cc_start: 0.8946 (p) cc_final: 0.8451 (m) REVERT: I 53 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7973 (p0) outliers start: 56 outliers final: 31 residues processed: 180 average time/residue: 0.0851 time to fit residues: 21.8520 Evaluate side-chains 165 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 27 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.152456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113872 restraints weight = 15730.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111959 restraints weight = 15871.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112892 restraints weight = 16192.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113734 restraints weight = 11752.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114020 restraints weight = 10277.992| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8869 Z= 0.113 Angle : 0.575 7.637 12106 Z= 0.296 Chirality : 0.043 0.148 1397 Planarity : 0.004 0.067 1541 Dihedral : 4.116 23.148 1241 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.19 % Favored : 88.38 % Rotamer: Outliers : 5.51 % Allowed : 29.44 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.26), residues: 1153 helix: 0.80 (0.34), residues: 256 sheet: -0.83 (0.32), residues: 313 loop : -2.06 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 87 TYR 0.013 0.001 TYR B 321 PHE 0.013 0.001 PHE B 210 TRP 0.022 0.001 TRP I 148 HIS 0.002 0.000 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8863) covalent geometry : angle 0.57498 / 0.30 (12094) SS BOND : bond 0.00324 / 0.26 ( 6) SS BOND : angle 0.69971 / 0.44 ( 12) hydrogen bonds : bond 0.04197 / 2.90 ( 251) hydrogen bonds : angle 5.44936 / 3.83 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8150 (ptm160) REVERT: A 162 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6911 (m90) REVERT: B 206 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7812 (pp) REVERT: B 378 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.7701 (t60) REVERT: G 49 SER cc_start: 0.9014 (p) cc_final: 0.8512 (m) outliers start: 50 outliers final: 31 residues processed: 170 average time/residue: 0.0842 time to fit residues: 20.4985 Evaluate side-chains 158 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 136 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 0.0370 chunk 11 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 102 optimal weight: 0.0170 chunk 64 optimal weight: 4.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 6 GLN I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113809 restraints weight = 15903.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111750 restraints weight = 15021.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112990 restraints weight = 15213.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113521 restraints weight = 10826.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.113793 restraints weight = 9821.659| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8869 Z= 0.109 Angle : 0.562 7.728 12106 Z= 0.287 Chirality : 0.042 0.149 1397 Planarity : 0.004 0.061 1541 Dihedral : 4.080 22.627 1241 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.45 % Favored : 88.12 % Rotamer: Outliers : 5.51 % Allowed : 29.99 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.26), residues: 1153 helix: 0.87 (0.34), residues: 250 sheet: -0.89 (0.32), residues: 309 loop : -2.02 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 87 TYR 0.021 0.001 TYR B 180 PHE 0.009 0.001 PHE B 210 TRP 0.019 0.001 TRP I 148 HIS 0.004 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8863) covalent geometry : angle 0.56231 / 0.29 (12094) SS BOND : bond 0.00370 / 0.30 ( 6) SS BOND : angle 0.68864 / 0.44 ( 12) hydrogen bonds : bond 0.03721 / 2.60 ( 251) hydrogen bonds : angle 5.09178 / 3.57 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8149 (ptm160) REVERT: B 206 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7790 (pp) REVERT: B 378 TRP cc_start: 0.8336 (OUTLIER) cc_final: 0.7695 (t60) REVERT: G 49 SER cc_start: 0.8961 (p) cc_final: 0.8504 (m) REVERT: I 53 ASN cc_start: 0.8206 (OUTLIER) cc_final: 0.7942 (p0) outliers start: 50 outliers final: 36 residues processed: 168 average time/residue: 0.0835 time to fit residues: 20.1583 Evaluate side-chains 170 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 134 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112903 restraints weight = 15885.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110942 restraints weight = 14504.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112082 restraints weight = 14951.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112689 restraints weight = 10670.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112948 restraints weight = 9732.305| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8869 Z= 0.118 Angle : 0.568 7.306 12106 Z= 0.290 Chirality : 0.044 0.384 1397 Planarity : 0.004 0.057 1541 Dihedral : 4.072 22.479 1241 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.54 % Favored : 88.03 % Rotamer: Outliers : 6.95 % Allowed : 28.67 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1153 helix: 0.91 (0.34), residues: 250 sheet: -0.94 (0.32), residues: 308 loop : -1.99 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 87 TYR 0.012 0.001 TYR B 321 PHE 0.025 0.001 PHE B 186 TRP 0.012 0.001 TRP B 284 HIS 0.006 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8863) covalent geometry : angle 0.56809 / 0.29 (12094) SS BOND : bond 0.00383 / 0.31 ( 6) SS BOND : angle 0.73278 / 0.47 ( 12) hydrogen bonds : bond 0.03653 / 2.55 ( 251) hydrogen bonds : angle 4.90879 / 3.44 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 136 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8154 (ptm160) REVERT: B 206 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7815 (pp) REVERT: B 207 ASP cc_start: 0.8388 (p0) cc_final: 0.8056 (p0) REVERT: B 348 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8779 (pp) REVERT: B 378 TRP cc_start: 0.8380 (OUTLIER) cc_final: 0.7676 (t60) REVERT: G 49 SER cc_start: 0.8996 (p) cc_final: 0.8540 (m) REVERT: I 53 ASN cc_start: 0.8201 (OUTLIER) cc_final: 0.7959 (p0) outliers start: 63 outliers final: 44 residues processed: 183 average time/residue: 0.0892 time to fit residues: 23.1202 Evaluate side-chains 176 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 134 CYS Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 0.0870 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS A 293 HIS I 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111682 restraints weight = 15819.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110034 restraints weight = 14824.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111085 restraints weight = 15108.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111657 restraints weight = 11161.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111849 restraints weight = 10039.347| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8869 Z= 0.132 Angle : 0.583 7.279 12106 Z= 0.297 Chirality : 0.044 0.328 1397 Planarity : 0.004 0.052 1541 Dihedral : 4.124 22.065 1241 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.06 % Favored : 87.51 % Rotamer: Outliers : 6.73 % Allowed : 28.89 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.25), residues: 1153 helix: 0.86 (0.34), residues: 253 sheet: -0.98 (0.30), residues: 323 loop : -2.07 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 87 TYR 0.018 0.001 TYR B 180 PHE 0.010 0.001 PHE B 186 TRP 0.014 0.001 TRP B 284 HIS 0.003 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 8863) covalent geometry : angle 0.58300 / 0.30 (12094) SS BOND : bond 0.00388 / 0.31 ( 6) SS BOND : angle 0.75392 / 0.49 ( 12) hydrogen bonds : bond 0.03661 / 2.57 ( 251) hydrogen bonds : angle 4.82462 / 3.39 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8174 (ptm160) REVERT: B 206 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7787 (pp) REVERT: B 207 ASP cc_start: 0.8460 (p0) cc_final: 0.8142 (p0) REVERT: B 348 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8744 (pp) REVERT: B 378 TRP cc_start: 0.8435 (OUTLIER) cc_final: 0.7770 (t60) REVERT: G 154 TYR cc_start: 0.5741 (p90) cc_final: 0.5297 (p90) REVERT: I 53 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7974 (p0) outliers start: 61 outliers final: 51 residues processed: 177 average time/residue: 0.0889 time to fit residues: 22.2330 Evaluate side-chains 181 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112156 restraints weight = 15836.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111364 restraints weight = 14577.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112012 restraints weight = 14576.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113020 restraints weight = 10729.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.113190 restraints weight = 9092.338| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8869 Z= 0.121 Angle : 0.582 7.237 12106 Z= 0.296 Chirality : 0.043 0.291 1397 Planarity : 0.004 0.051 1541 Dihedral : 4.112 21.732 1241 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.71 % Favored : 87.86 % Rotamer: Outliers : 7.06 % Allowed : 29.00 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.25), residues: 1153 helix: 0.98 (0.34), residues: 246 sheet: -0.97 (0.31), residues: 309 loop : -1.96 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 87 TYR 0.012 0.001 TYR B 321 PHE 0.009 0.001 PHE B 115 TRP 0.012 0.001 TRP B 284 HIS 0.007 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8863) covalent geometry : angle 0.58205 / 0.30 (12094) SS BOND : bond 0.00366 / 0.29 ( 6) SS BOND : angle 0.69798 / 0.46 ( 12) hydrogen bonds : bond 0.03514 / 2.46 ( 251) hydrogen bonds : angle 4.72526 / 3.33 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 132 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8231 (ptm160) REVERT: B 206 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7771 (pp) REVERT: B 207 ASP cc_start: 0.8412 (p0) cc_final: 0.8083 (p0) REVERT: B 348 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8771 (pp) REVERT: B 378 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7792 (t60) REVERT: I 53 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7992 (p0) outliers start: 64 outliers final: 52 residues processed: 181 average time/residue: 0.0755 time to fit residues: 19.9137 Evaluate side-chains 183 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 126 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 6 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.7132 > 50:) overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS B 111 GLN B 340 ASN I 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109611 restraints weight = 15744.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109123 restraints weight = 12168.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108909 restraints weight = 10034.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109047 restraints weight = 9571.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109750 restraints weight = 8885.898| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8869 Z= 0.115 Angle : 0.585 7.732 12106 Z= 0.297 Chirality : 0.043 0.282 1397 Planarity : 0.004 0.050 1541 Dihedral : 4.133 23.154 1241 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.27 % Favored : 88.29 % Rotamer: Outliers : 6.39 % Allowed : 30.21 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.25), residues: 1153 helix: 1.08 (0.34), residues: 245 sheet: -0.97 (0.31), residues: 310 loop : -1.95 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 87 TYR 0.019 0.001 TYR B 180 PHE 0.009 0.001 PHE G 68 TRP 0.014 0.001 TRP I 148 HIS 0.005 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.11 ( 8863) covalent geometry : angle 0.58495 / 0.30 (12094) SS BOND : bond 0.00322 / 0.24 ( 6) SS BOND : angle 0.86320 / 0.52 ( 12) hydrogen bonds : bond 0.03374 / 2.36 ( 251) hydrogen bonds : angle 4.66158 / 3.28 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 134 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8298 (ptm160) REVERT: B 206 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7679 (pp) REVERT: B 207 ASP cc_start: 0.8568 (p0) cc_final: 0.8322 (p0) REVERT: B 348 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B 378 TRP cc_start: 0.8431 (OUTLIER) cc_final: 0.7666 (t60) REVERT: G 154 TYR cc_start: 0.5518 (p90) cc_final: 0.4914 (p90) REVERT: I 53 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.8017 (p0) outliers start: 58 outliers final: 49 residues processed: 177 average time/residue: 0.0714 time to fit residues: 18.4499 Evaluate side-chains 182 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 128 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 7.9990 chunk 59 optimal weight: 0.0270 chunk 90 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 52 optimal weight: 0.0870 overall best weight: 0.8418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 HIS B 119 HIS B 340 ASN I 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.113298 restraints weight = 15726.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.111484 restraints weight = 14871.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112696 restraints weight = 15415.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.113170 restraints weight = 10638.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113412 restraints weight = 10053.177| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8869 Z= 0.132 Angle : 0.612 8.265 12106 Z= 0.309 Chirality : 0.043 0.271 1397 Planarity : 0.004 0.048 1541 Dihedral : 4.177 22.722 1241 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.45 % Favored : 88.03 % Rotamer: Outliers : 6.62 % Allowed : 30.43 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.25), residues: 1153 helix: 1.07 (0.34), residues: 245 sheet: -1.09 (0.30), residues: 324 loop : -1.96 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 87 TYR 0.013 0.001 TYR G 80 PHE 0.009 0.001 PHE B 115 TRP 0.012 0.001 TRP B 284 HIS 0.006 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 8863) covalent geometry : angle 0.61127 / 0.31 (12094) SS BOND : bond 0.00370 / 0.28 ( 6) SS BOND : angle 0.96664 / 0.60 ( 12) hydrogen bonds : bond 0.03495 / 2.45 ( 251) hydrogen bonds : angle 4.67971 / 3.30 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 125 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8169 (ptm160) REVERT: B 206 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7761 (pp) REVERT: B 207 ASP cc_start: 0.8351 (p0) cc_final: 0.8045 (p0) REVERT: B 348 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8728 (pp) REVERT: B 378 TRP cc_start: 0.8474 (OUTLIER) cc_final: 0.7751 (t60) REVERT: G 19 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8616 (mtp180) REVERT: I 53 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.8000 (p0) outliers start: 60 outliers final: 52 residues processed: 170 average time/residue: 0.0740 time to fit residues: 17.7664 Evaluate side-chains 181 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 164 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.0170 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 HIS I 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.152780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114181 restraints weight = 15732.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110963 restraints weight = 14872.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112289 restraints weight = 15345.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113229 restraints weight = 10631.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113597 restraints weight = 9340.429| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 8869 Z= 0.120 Angle : 0.603 8.658 12106 Z= 0.304 Chirality : 0.044 0.273 1397 Planarity : 0.004 0.048 1541 Dihedral : 4.152 22.567 1241 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.93 % Favored : 88.55 % Rotamer: Outliers : 6.73 % Allowed : 30.21 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.25), residues: 1153 helix: 1.11 (0.34), residues: 245 sheet: -1.06 (0.30), residues: 324 loop : -1.94 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 87 TYR 0.020 0.001 TYR B 180 PHE 0.011 0.001 PHE B 115 TRP 0.014 0.001 TRP B 284 HIS 0.007 0.001 HIS B 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.12 ( 8863) covalent geometry : angle 0.60284 / 0.30 (12094) SS BOND : bond 0.00350 / 0.27 ( 6) SS BOND : angle 0.91666 / 0.57 ( 12) hydrogen bonds : bond 0.03385 / 2.38 ( 251) hydrogen bonds : angle 4.62358 / 3.26 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8240 (ptm160) REVERT: B 206 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7781 (pp) REVERT: B 207 ASP cc_start: 0.8399 (p0) cc_final: 0.8107 (p0) REVERT: B 348 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8765 (pp) REVERT: B 378 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7694 (t60) REVERT: G 154 TYR cc_start: 0.5792 (p90) cc_final: 0.5327 (p90) REVERT: I 51 ASP cc_start: 0.8522 (t0) cc_final: 0.8288 (t0) REVERT: I 53 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7798 (p0) outliers start: 61 outliers final: 49 residues processed: 174 average time/residue: 0.0767 time to fit residues: 19.0226 Evaluate side-chains 179 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 HIS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 321 TYR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 346 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 35 GLN Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 53 ASN Chi-restraints excluded: chain I residue 63 PHE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 202 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 0.1980 chunk 82 optimal weight: 0.0170 chunk 19 optimal weight: 0.0870 chunk 41 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.0810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 111 GLN B 119 HIS I 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.155184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115382 restraints weight = 15747.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.114254 restraints weight = 14220.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114987 restraints weight = 13459.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115826 restraints weight = 10401.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116054 restraints weight = 8983.221| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8869 Z= 0.112 Angle : 0.602 8.803 12106 Z= 0.301 Chirality : 0.043 0.284 1397 Planarity : 0.004 0.048 1541 Dihedral : 4.014 22.198 1241 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.80 % Favored : 89.77 % Rotamer: Outliers : 4.74 % Allowed : 32.41 % Favored : 62.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.26), residues: 1153 helix: 1.21 (0.35), residues: 244 sheet: -0.97 (0.31), residues: 307 loop : -1.87 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 87 TYR 0.019 0.001 TYR I 140 PHE 0.008 0.001 PHE B 210 TRP 0.014 0.001 TRP B 284 HIS 0.003 0.001 HIS G 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 8863) covalent geometry : angle 0.60190 / 0.30 (12094) SS BOND : bond 0.00327 / 0.25 ( 6) SS BOND : angle 0.82091 / 0.49 ( 12) hydrogen bonds : bond 0.02982 / 2.08 ( 251) hydrogen bonds : angle 4.43721 / 3.11 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1543.48 seconds wall clock time: 27 minutes 24.31 seconds (1644.31 seconds total)