Starting phenix.real_space_refine on Fri Oct 23 08:51:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xix_66922/10_2026/9xix_66922.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xix_66922/10_2026/9xix_66922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xix_66922/10_2026/9xix_66922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xix_66922/10_2026/9xix_66922.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xix_66922/10_2026/9xix_66922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xix_66922/10_2026/9xix_66922.map" } resolution = 2.58 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= 0.023 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 64 5.16 5 C 5807 2.51 5 N 1545 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9083 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1875 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 423 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1761 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "R" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2370 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.88, per 1000 atoms: 0.21 Number of scatterers: 9083 At special positions: 0 Unit cell: (93.656, 124.196, 143.538, 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 64 16.00 O 1667 8.00 N 1545 7.00 C 5807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " 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: 0.88 Conformation dependent library (CDL) restraints added in 321.1 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 38.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 5 through 37 removed outlier: 3.789A pdb=" N ALA A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.404A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.578A pdb=" N PHE A 264 " --> pdb=" O TYR A 261 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 275 through 284 removed outlier: 3.871A pdb=" N MET A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.459A pdb=" N TYR A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 316 removed outlier: 3.632A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.619A pdb=" N LYS A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.595A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 44 through 48 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.571A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'R' and resid 25 through 59 Proline residue: R 34 - end of helix removed outlier: 3.644A pdb=" N ILE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 3.752A pdb=" N VAL R 70 " --> pdb=" O CYS R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.519A pdb=" N TRP R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 136 removed outlier: 3.784A pdb=" N CYS R 104 " --> pdb=" O ALA R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 182 through 197 removed outlier: 4.375A pdb=" N ILE R 186 " --> pdb=" O VAL R 182 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 217 Processing helix chain 'R' and resid 222 through 256 Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 262 through 281 removed outlier: 3.728A pdb=" N SER R 278 " --> pdb=" O ILE R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 292 Proline residue: R 288 - end of helix removed outlier: 3.539A pdb=" N TYR R 291 " --> pdb=" O ASN R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 298 through 310 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 3.546A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 229 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.721A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.843A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.963A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.675A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.953A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.552A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.708A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.079A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.079A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.194A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D 213 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.194A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D 213 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR D 226 " --> pdb=" O GLN D 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 165 through 169 removed outlier: 5.002A pdb=" N THR R 167 " --> pdb=" O MET R 174 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N MET R 174 " --> pdb=" O THR R 167 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS R 169 " --> pdb=" O GLN R 172 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.14 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: 2923 1.34 - 1.46: 2258 1.46 - 1.58: 4007 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 9280 Sorted by residual: bond pdb=" CG ARG B 137 " pdb=" CD ARG B 137 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.87e-01 bond pdb=" C MET R 115 " pdb=" O MET R 115 " ideal model delta sigma weight residual 1.236 1.246 -0.009 1.15e-02 7.56e+03 6.58e-01 bond pdb=" C LEU R 230 " pdb=" O LEU R 230 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.21e-01 bond pdb=" CA LYS R 33 " pdb=" C LYS R 33 " ideal model delta sigma weight residual 1.520 1.529 -0.009 1.23e-02 6.61e+03 5.16e-01 bond pdb=" C ILE R 122 " pdb=" O ILE R 122 " ideal model delta sigma weight residual 1.237 1.244 -0.008 1.13e-02 7.83e+03 4.56e-01 ... (remaining 9275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 12062 1.14 - 2.27: 423 2.27 - 3.41: 71 3.41 - 4.55: 13 4.55 - 5.69: 13 Bond angle restraints: 12582 Sorted by residual: angle pdb=" CA GLY D 114 " pdb=" C GLY D 114 " pdb=" O GLY D 114 " ideal model delta sigma weight residual 122.22 120.45 1.77 6.50e-01 2.37e+00 7.45e+00 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 125.70 -4.16 1.91e+00 2.74e-01 4.75e+00 angle pdb=" C ILE B 123 " pdb=" N TYR B 124 " pdb=" CA TYR B 124 " ideal model delta sigma weight residual 122.93 125.92 -2.99 1.45e+00 4.76e-01 4.25e+00 angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" C MET D 180 " ideal model delta sigma weight residual 110.80 115.05 -4.25 2.13e+00 2.20e-01 3.97e+00 angle pdb=" N LEU R 242 " pdb=" CA LEU R 242 " pdb=" C LEU R 242 " ideal model delta sigma weight residual 109.81 114.18 -4.37 2.21e+00 2.05e-01 3.91e+00 ... (remaining 12577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5103 17.83 - 35.67: 329 35.67 - 53.50: 60 53.50 - 71.34: 11 71.34 - 89.17: 6 Dihedral angle restraints: 5509 sinusoidal: 2147 harmonic: 3362 Sorted by residual: dihedral pdb=" CA ARG D 179 " pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 801 0.028 - 0.055: 371 0.055 - 0.083: 149 0.083 - 0.111: 84 0.111 - 0.139: 25 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA VAL D 37 " pdb=" N VAL D 37 " pdb=" C VAL D 37 " pdb=" CB VAL D 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1427 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 192 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 193 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 193 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 193 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO B 236 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 106 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO D 107 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 107 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 107 " 0.028 5.00e-02 4.00e+02 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 5555 3.05 - 3.51: 8764 3.51 - 3.98: 13910 3.98 - 4.44: 17322 4.44 - 4.90: 27516 Nonbonded interactions: 73067 Sorted by model distance: nonbonded pdb=" N THR B 184 " pdb=" OG1 THR B 184 " model vdw 2.588 2.496 nonbonded pdb=" N TYR D 102 " pdb=" O TYR D 102 " model vdw 2.590 2.496 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.599 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.611 3.040 nonbonded pdb=" C THR D 63 " pdb=" OG1 THR D 63 " model vdw 2.612 2.616 ... (remaining 73062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.850 Find NCS groups from input model: 0.060 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:10.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 0.029 9284 Z= 0.136 Angle : 0.538 5.686 12590 Z= 0.294 Chirality : 0.043 0.139 1430 Planarity : 0.004 0.052 1588 Dihedral : 12.628 89.174 3325 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.42 % Allowed : 7.17 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.96 (0.24), residues: 1134 helix: 2.35 (0.25), residues: 409 sheet: 0.58 (0.30), residues: 283 loop : -1.00 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 38 TYR 0.009 0.001 TYR D 178 PHE 0.017 0.002 PHE B 151 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 ( 9280) covalent geometry : angle 0.53748 / 0.29 (12582) SS BOND : bond 0.00574 / 0.34 ( 4) SS BOND : angle 1.37467 / 0.73 ( 8) hydrogen bonds : bond 0.13265 / 9.25 ( 463) hydrogen bonds : angle 5.59821 / 3.95 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.314 Fit side-chains REVERT: A 19 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8190 (mt-10) REVERT: A 191 GLU cc_start: 0.8411 (tt0) cc_final: 0.8102 (tt0) REVERT: A 256 ARG cc_start: 0.7800 (ttt90) cc_final: 0.7135 (ttp-170) REVERT: A 296 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5751 (p0) REVERT: A 345 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7527 (mmtt) REVERT: A 350 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: A 354 LYS cc_start: 0.8120 (mttt) cc_final: 0.7756 (mmtt) REVERT: B 23 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7501 (mtmt) REVERT: B 46 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7659 (mtp180) REVERT: B 55 LEU cc_start: 0.8014 (pp) cc_final: 0.7557 (mt) REVERT: B 146 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 175 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8375 (mm110) REVERT: B 184 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8489 (p) REVERT: C 29 LYS cc_start: 0.8393 (mmtp) cc_final: 0.7959 (mmtt) REVERT: D 34 MET cc_start: 0.8468 (mmp) cc_final: 0.8165 (mmm) REVERT: D 43 LYS cc_start: 0.7333 (mmtm) cc_final: 0.6441 (mttp) REVERT: D 93 MET cc_start: 0.8403 (ttp) cc_final: 0.7727 (tpp) REVERT: D 113 GLN cc_start: 0.7502 (mt0) cc_final: 0.6862 (mm110) REVERT: D 211 ASP cc_start: 0.8025 (m-30) cc_final: 0.7805 (m-30) REVERT: R 79 ASP cc_start: 0.8566 (m-30) cc_final: 0.8344 (m-30) REVERT: R 90 MET cc_start: 0.6550 (mtm) cc_final: 0.6228 (mtm) REVERT: R 147 PHE cc_start: 0.6993 (m-80) cc_final: 0.6577 (m-80) REVERT: R 164 MET cc_start: 0.4083 (ptm) cc_final: 0.3165 (mmm) REVERT: R 184 TYR cc_start: 0.5845 (t80) cc_final: 0.5415 (t80) REVERT: R 222 HIS cc_start: 0.8323 (m90) cc_final: 0.8096 (m90) outliers start: 24 outliers final: 10 residues processed: 156 average time/residue: 0.5446 time to fit residues: 90.8449 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain L residue 1 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN D 3 GLN R 283 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138107 restraints weight = 9736.852| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 1.91 r_work: 0.3588 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9284 Z= 0.158 Angle : 0.576 5.885 12590 Z= 0.310 Chirality : 0.044 0.143 1430 Planarity : 0.004 0.055 1588 Dihedral : 6.758 73.622 1285 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.64 % Allowed : 11.01 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.02 (0.24), residues: 1134 helix: 2.43 (0.25), residues: 412 sheet: 0.64 (0.30), residues: 278 loop : -1.03 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 148 TYR 0.017 0.002 TYR R 92 PHE 0.019 0.002 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 9280) covalent geometry : angle 0.57364 / 0.31 (12582) SS BOND : bond 0.00674 / 0.41 ( 4) SS BOND : angle 1.98174 / 1.03 ( 8) hydrogen bonds : bond 0.05697 / 3.93 ( 463) hydrogen bonds : angle 4.66146 / 3.26 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.367 Fit side-chains REVERT: A 19 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 191 GLU cc_start: 0.8399 (tt0) cc_final: 0.8094 (tt0) REVERT: A 196 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4780 (tm) REVERT: A 237 GLN cc_start: 0.6295 (mt0) cc_final: 0.6041 (mt0) REVERT: A 256 ARG cc_start: 0.7225 (ttt90) cc_final: 0.6459 (ttp-170) REVERT: A 345 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7079 (mmtt) REVERT: A 350 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.6968 (mp10) REVERT: A 354 LYS cc_start: 0.8001 (mttt) cc_final: 0.7385 (mmtt) REVERT: B 23 LYS cc_start: 0.8119 (ttmt) cc_final: 0.7646 (mtmt) REVERT: B 46 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7798 (mtp180) REVERT: B 55 LEU cc_start: 0.8063 (pp) cc_final: 0.7618 (mt) REVERT: B 146 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 175 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8428 (mm110) REVERT: B 184 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8458 (p) REVERT: B 318 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8731 (mp) REVERT: D 34 MET cc_start: 0.8505 (mmp) cc_final: 0.8280 (mmm) REVERT: D 43 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7157 (mptt) REVERT: D 93 MET cc_start: 0.8575 (ttp) cc_final: 0.8056 (tpp) REVERT: D 113 GLN cc_start: 0.7749 (mt0) cc_final: 0.7338 (mm110) REVERT: D 174 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7897 (pp30) REVERT: R 79 ASP cc_start: 0.8397 (m-30) cc_final: 0.8125 (m-30) REVERT: R 90 MET cc_start: 0.6477 (mtm) cc_final: 0.6246 (mtm) REVERT: R 147 PHE cc_start: 0.6720 (m-80) cc_final: 0.6261 (m-80) REVERT: R 164 MET cc_start: 0.3859 (ptm) cc_final: 0.3037 (mmm) REVERT: R 184 TYR cc_start: 0.5525 (t80) cc_final: 0.5081 (t80) outliers start: 36 outliers final: 13 residues processed: 146 average time/residue: 0.5447 time to fit residues: 84.9726 Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [38, 47, 69, 70, 48, 36, 37, 10, 57, 89, 28] chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 0.0060 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.193964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141027 restraints weight = 9738.571| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.92 r_work: 0.3630 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9284 Z= 0.111 Angle : 0.501 5.673 12590 Z= 0.272 Chirality : 0.041 0.138 1430 Planarity : 0.004 0.054 1588 Dihedral : 6.297 72.198 1282 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.13 % Allowed : 12.32 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.26 (0.25), residues: 1134 helix: 2.69 (0.25), residues: 413 sheet: 0.72 (0.30), residues: 283 loop : -0.95 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 148 TYR 0.012 0.001 TYR D 178 PHE 0.015 0.001 PHE B 151 TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9280) covalent geometry : angle 0.49968 / 0.27 (12582) SS BOND : bond 0.00420 / 0.26 ( 4) SS BOND : angle 1.55949 / 0.83 ( 8) hydrogen bonds : bond 0.04681 / 3.23 ( 463) hydrogen bonds : angle 4.36058 / 3.04 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.340 Fit side-chains REVERT: A 19 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7999 (mt-10) REVERT: A 191 GLU cc_start: 0.8349 (tt0) cc_final: 0.7995 (tt0) REVERT: A 237 GLN cc_start: 0.6234 (mt0) cc_final: 0.5974 (mt0) REVERT: A 256 ARG cc_start: 0.7201 (ttt90) cc_final: 0.6431 (ttp-170) REVERT: A 345 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7127 (mmtt) REVERT: A 350 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: A 354 LYS cc_start: 0.8037 (mttt) cc_final: 0.7408 (mmtt) REVERT: B 23 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7663 (mtmt) REVERT: B 46 ARG cc_start: 0.8047 (mtm180) cc_final: 0.7781 (mtp180) REVERT: B 55 LEU cc_start: 0.7994 (pp) cc_final: 0.7554 (mt) REVERT: B 146 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8442 (mm) REVERT: B 172 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7347 (tp30) REVERT: B 184 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 217 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8274 (pmm) REVERT: B 318 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 59 ASN cc_start: 0.8011 (t0) cc_final: 0.7809 (t160) REVERT: D 43 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7091 (mttp) REVERT: D 93 MET cc_start: 0.8519 (ttp) cc_final: 0.7986 (tpp) REVERT: D 113 GLN cc_start: 0.7745 (mt0) cc_final: 0.7369 (mm110) REVERT: D 174 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7877 (pp30) REVERT: R 90 MET cc_start: 0.6435 (mtm) cc_final: 0.6201 (mtm) REVERT: R 147 PHE cc_start: 0.6700 (m-80) cc_final: 0.6239 (m-80) REVERT: R 164 MET cc_start: 0.4131 (ptm) cc_final: 0.3199 (mmm) REVERT: R 184 TYR cc_start: 0.5552 (t80) cc_final: 0.5024 (t80) outliers start: 31 outliers final: 10 residues processed: 145 average time/residue: 0.5510 time to fit residues: 85.4060 Evaluate side-chains 131 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [19, 6, 85, 78, 111, 69, 60, 72, 81, 51, 18] chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.191067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138837 restraints weight = 9808.040| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.86 r_work: 0.3589 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9284 Z= 0.164 Angle : 0.590 8.229 12590 Z= 0.318 Chirality : 0.044 0.219 1430 Planarity : 0.004 0.057 1588 Dihedral : 6.039 66.016 1276 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.94 % Allowed : 12.42 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1134 helix: 2.60 (0.24), residues: 410 sheet: 0.72 (0.30), residues: 280 loop : -1.11 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 148 TYR 0.010 0.002 TYR A 356 PHE 0.018 0.002 PHE B 151 TRP 0.013 0.002 TRP B 169 HIS 0.005 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9280) covalent geometry : angle 0.57960 / 0.31 (12582) SS BOND : bond 0.00753 / 0.43 ( 4) SS BOND : angle 4.43823 / 2.31 ( 8) hydrogen bonds : bond 0.05525 / 3.75 ( 463) hydrogen bonds : angle 4.53023 / 3.15 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.250 Fit side-chains REVERT: A 19 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 28 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7877 (tp40) REVERT: A 191 GLU cc_start: 0.8416 (tt0) cc_final: 0.7951 (tt0) REVERT: A 196 LEU cc_start: 0.5251 (OUTLIER) cc_final: 0.4813 (tm) REVERT: A 237 GLN cc_start: 0.6351 (mt0) cc_final: 0.6068 (mt0) REVERT: A 256 ARG cc_start: 0.7235 (ttt90) cc_final: 0.6420 (ttp-170) REVERT: A 316 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7416 (mt) REVERT: A 345 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7129 (mmtt) REVERT: A 350 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: A 354 LYS cc_start: 0.7993 (mttt) cc_final: 0.7373 (mmtt) REVERT: B 23 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7662 (mtmt) REVERT: B 46 ARG cc_start: 0.8099 (mtm180) cc_final: 0.7774 (mtp180) REVERT: B 55 LEU cc_start: 0.8077 (pp) cc_final: 0.7661 (mt) REVERT: B 134 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7637 (ptt-90) REVERT: B 184 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8437 (p) REVERT: B 217 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8290 (pmm) REVERT: B 318 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8696 (mp) REVERT: C 62 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.5315 (ptt90) REVERT: D 43 LYS cc_start: 0.7836 (mmtm) cc_final: 0.7196 (mptt) REVERT: D 93 MET cc_start: 0.8581 (ttp) cc_final: 0.8026 (tpp) REVERT: D 113 GLN cc_start: 0.7806 (mt0) cc_final: 0.7381 (mm110) REVERT: D 174 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7853 (pp30) REVERT: R 147 PHE cc_start: 0.6796 (m-80) cc_final: 0.6335 (m-80) REVERT: R 164 MET cc_start: 0.3940 (ptm) cc_final: 0.3091 (mmm) REVERT: R 184 TYR cc_start: 0.5427 (t80) cc_final: 0.4878 (t80) outliers start: 39 outliers final: 18 residues processed: 141 average time/residue: 0.5463 time to fit residues: 82.1973 Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 62 ARG Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [22, 97, 33, 12, 80, 68, 98, 10, 20, 87, 83] chunk 22 optimal weight: 2.9990 chunk 97 optimal weight: 0.0670 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.192333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140549 restraints weight = 9730.241| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.86 r_work: 0.3610 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9284 Z= 0.127 Angle : 0.534 5.861 12590 Z= 0.288 Chirality : 0.042 0.140 1430 Planarity : 0.004 0.056 1588 Dihedral : 5.856 63.801 1276 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.33 % Allowed : 13.74 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.20 (0.24), residues: 1134 helix: 2.62 (0.24), residues: 418 sheet: 0.74 (0.30), residues: 280 loop : -1.03 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 148 TYR 0.021 0.001 TYR R 92 PHE 0.016 0.001 PHE B 151 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9280) covalent geometry : angle 0.52838 / 0.29 (12582) SS BOND : bond 0.00459 / 0.28 ( 4) SS BOND : angle 2.97822 / 1.60 ( 8) hydrogen bonds : bond 0.04931 / 3.38 ( 463) hydrogen bonds : angle 4.38766 / 3.06 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.368 Fit side-chains REVERT: A 19 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8024 (mt-10) REVERT: A 28 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7846 (tp40) REVERT: A 191 GLU cc_start: 0.8428 (tt0) cc_final: 0.8105 (tt0) REVERT: A 196 LEU cc_start: 0.5230 (OUTLIER) cc_final: 0.4815 (tm) REVERT: A 256 ARG cc_start: 0.7220 (ttt90) cc_final: 0.6418 (ttp-170) REVERT: A 316 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7351 (mt) REVERT: A 345 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7124 (mmtt) REVERT: A 350 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.6917 (mp10) REVERT: A 354 LYS cc_start: 0.7983 (mttt) cc_final: 0.7366 (mmtt) REVERT: B 23 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7637 (mtmt) REVERT: B 46 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7804 (mtp180) REVERT: B 55 LEU cc_start: 0.8038 (pp) cc_final: 0.7640 (mt) REVERT: B 172 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7364 (tp30) REVERT: B 184 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8427 (p) REVERT: B 217 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8212 (pmm) REVERT: B 318 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (mp) REVERT: D 43 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7192 (mptt) REVERT: D 93 MET cc_start: 0.8548 (ttp) cc_final: 0.8019 (tpp) REVERT: D 113 GLN cc_start: 0.7819 (mt0) cc_final: 0.7389 (mm110) REVERT: D 157 ASN cc_start: 0.7563 (m-40) cc_final: 0.6900 (m-40) REVERT: D 174 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7857 (pp30) REVERT: R 92 TYR cc_start: 0.6582 (t80) cc_final: 0.6277 (t80) REVERT: R 147 PHE cc_start: 0.6779 (m-80) cc_final: 0.6353 (m-80) REVERT: R 164 MET cc_start: 0.4135 (ptm) cc_final: 0.3152 (mmm) REVERT: R 184 TYR cc_start: 0.5403 (t80) cc_final: 0.4890 (t80) outliers start: 33 outliers final: 14 residues processed: 137 average time/residue: 0.5318 time to fit residues: 77.9432 Evaluate side-chains 136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [9, 82, 95, 36, 91, 31, 55, 43, 90, 27, 108] chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 0.0030 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 340 ASN C 59 ASN D 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.190416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.138484 restraints weight = 9694.877| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.83 r_work: 0.3589 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9284 Z= 0.167 Angle : 0.584 5.991 12590 Z= 0.314 Chirality : 0.044 0.144 1430 Planarity : 0.004 0.057 1588 Dihedral : 5.968 66.488 1274 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.84 % Allowed : 13.84 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1134 helix: 2.54 (0.24), residues: 412 sheet: 0.71 (0.30), residues: 280 loop : -1.16 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 179 TYR 0.018 0.002 TYR R 92 PHE 0.019 0.002 PHE B 151 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 9280) covalent geometry : angle 0.57951 / 0.31 (12582) SS BOND : bond 0.00635 / 0.39 ( 4) SS BOND : angle 3.07753 / 1.64 ( 8) hydrogen bonds : bond 0.05538 / 3.79 ( 463) hydrogen bonds : angle 4.52372 / 3.16 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.341 Fit side-chains REVERT: A 19 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 28 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7836 (tp-100) REVERT: A 57 LYS cc_start: 0.6759 (mttp) cc_final: 0.6556 (mttm) REVERT: A 191 GLU cc_start: 0.8465 (tt0) cc_final: 0.8169 (tt0) REVERT: A 196 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4776 (tm) REVERT: A 256 ARG cc_start: 0.7218 (ttt90) cc_final: 0.6397 (ttp-170) REVERT: A 316 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7450 (mt) REVERT: A 345 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7136 (mmtt) REVERT: A 350 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: A 354 LYS cc_start: 0.7991 (mttt) cc_final: 0.7380 (mmtt) REVERT: B 23 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7677 (mtmt) REVERT: B 46 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7778 (mtp180) REVERT: B 55 LEU cc_start: 0.8092 (pp) cc_final: 0.7670 (mt) REVERT: B 184 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 217 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8277 (pmm) REVERT: B 318 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 338 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8389 (mp) REVERT: D 43 LYS cc_start: 0.7834 (mmtm) cc_final: 0.7150 (mptt) REVERT: D 93 MET cc_start: 0.8595 (ttp) cc_final: 0.8041 (tpp) REVERT: D 113 GLN cc_start: 0.7808 (mt0) cc_final: 0.7397 (mm110) REVERT: D 174 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7833 (pp30) REVERT: R 92 TYR cc_start: 0.6599 (t80) cc_final: 0.6302 (t80) REVERT: R 147 PHE cc_start: 0.6795 (m-80) cc_final: 0.6393 (m-80) REVERT: R 164 MET cc_start: 0.4049 (ptm) cc_final: 0.3149 (mmm) REVERT: R 184 TYR cc_start: 0.5402 (t80) cc_final: 0.4932 (t80) outliers start: 38 outliers final: 20 residues processed: 143 average time/residue: 0.5550 time to fit residues: 84.8076 Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [61, 13, 38, 77, 48, 29, 50, 73, 33, 40, 0] chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN B 340 ASN D 3 GLN R 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.192140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140282 restraints weight = 9780.625| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.86 r_work: 0.3608 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9284 Z= 0.125 Angle : 0.531 6.454 12590 Z= 0.286 Chirality : 0.042 0.138 1430 Planarity : 0.004 0.056 1588 Dihedral : 5.742 63.261 1274 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.33 % Allowed : 14.75 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.19 (0.25), residues: 1134 helix: 2.68 (0.24), residues: 413 sheet: 0.71 (0.30), residues: 285 loop : -1.08 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.017 0.001 TYR R 92 PHE 0.016 0.001 PHE B 151 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 9280) covalent geometry : angle 0.52732 / 0.28 (12582) SS BOND : bond 0.00503 / 0.29 ( 4) SS BOND : angle 2.41730 / 1.31 ( 8) hydrogen bonds : bond 0.04856 / 3.33 ( 463) hydrogen bonds : angle 4.36411 / 3.05 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8038 (mt-10) REVERT: A 28 GLN cc_start: 0.8069 (tp-100) cc_final: 0.7784 (tp-100) REVERT: A 57 LYS cc_start: 0.6765 (mttp) cc_final: 0.6548 (mttm) REVERT: A 191 GLU cc_start: 0.8458 (tt0) cc_final: 0.7996 (tt0) REVERT: A 196 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4803 (tm) REVERT: A 256 ARG cc_start: 0.7158 (ttt90) cc_final: 0.6339 (ttp-170) REVERT: A 316 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7362 (mt) REVERT: A 345 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7125 (mmtt) REVERT: A 350 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.6905 (mp10) REVERT: A 354 LYS cc_start: 0.7980 (mttt) cc_final: 0.7352 (mmtt) REVERT: B 23 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7636 (mtmt) REVERT: B 46 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7818 (mtp180) REVERT: B 55 LEU cc_start: 0.8022 (pp) cc_final: 0.7605 (mt) REVERT: B 146 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 172 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7368 (tp30) REVERT: B 184 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 217 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8200 (pmm) REVERT: B 318 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8677 (mp) REVERT: D 43 LYS cc_start: 0.7785 (mmtm) cc_final: 0.7160 (mptt) REVERT: D 93 MET cc_start: 0.8548 (ttp) cc_final: 0.8020 (tpp) REVERT: D 113 GLN cc_start: 0.7825 (mt0) cc_final: 0.7392 (mm110) REVERT: D 157 ASN cc_start: 0.7561 (m-40) cc_final: 0.6938 (m-40) REVERT: D 174 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7804 (pp30) REVERT: R 92 TYR cc_start: 0.6554 (t80) cc_final: 0.6323 (t80) REVERT: R 147 PHE cc_start: 0.6741 (m-80) cc_final: 0.6334 (m-80) REVERT: R 164 MET cc_start: 0.4161 (ptm) cc_final: 0.3167 (mmm) REVERT: R 184 TYR cc_start: 0.5391 (t80) cc_final: 0.4901 (t80) outliers start: 33 outliers final: 17 residues processed: 142 average time/residue: 0.5485 time to fit residues: 83.2047 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [105, 83, 33, 103, 11, 39, 64, 5, 89, 50, 107] chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.187526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130953 restraints weight = 9178.768| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.76 r_work: 0.3377 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9284 Z= 0.153 Angle : 0.566 6.911 12590 Z= 0.304 Chirality : 0.043 0.142 1430 Planarity : 0.004 0.056 1588 Dihedral : 5.867 65.740 1274 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.93 % Allowed : 15.66 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1134 helix: 2.63 (0.24), residues: 416 sheet: 0.71 (0.30), residues: 280 loop : -1.15 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.016 0.002 TYR R 92 PHE 0.021 0.002 PHE R 150 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 9280) covalent geometry : angle 0.56329 / 0.30 (12582) SS BOND : bond 0.00628 / 0.38 ( 4) SS BOND : angle 2.43899 / 1.25 ( 8) hydrogen bonds : bond 0.05298 / 3.63 ( 463) hydrogen bonds : angle 4.46098 / 3.12 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 28 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7814 (tp-100) REVERT: A 57 LYS cc_start: 0.6524 (mttp) cc_final: 0.6316 (mttm) REVERT: A 191 GLU cc_start: 0.8455 (tt0) cc_final: 0.8011 (tt0) REVERT: A 196 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4734 (tm) REVERT: A 256 ARG cc_start: 0.7087 (ttt90) cc_final: 0.6222 (ttp-170) REVERT: A 316 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7230 (mt) REVERT: A 345 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7051 (mmtt) REVERT: A 350 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: A 354 LYS cc_start: 0.7969 (mttt) cc_final: 0.7313 (mmtt) REVERT: B 23 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7549 (mtmt) REVERT: B 46 ARG cc_start: 0.8121 (mtm180) cc_final: 0.7795 (mtp180) REVERT: B 55 LEU cc_start: 0.8107 (pp) cc_final: 0.7660 (mt) REVERT: B 146 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 184 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8453 (p) REVERT: B 217 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8217 (pmm) REVERT: B 318 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8747 (mp) REVERT: D 43 LYS cc_start: 0.7808 (mmtm) cc_final: 0.7087 (mptt) REVERT: D 93 MET cc_start: 0.8527 (ttp) cc_final: 0.7962 (tpp) REVERT: D 113 GLN cc_start: 0.7869 (mt0) cc_final: 0.7424 (mm110) REVERT: D 174 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7848 (pp30) REVERT: R 147 PHE cc_start: 0.6614 (m-80) cc_final: 0.6174 (m-80) REVERT: R 164 MET cc_start: 0.4109 (ptm) cc_final: 0.3123 (mmm) REVERT: R 184 TYR cc_start: 0.5290 (t80) cc_final: 0.4846 (t80) outliers start: 29 outliers final: 18 residues processed: 135 average time/residue: 0.5649 time to fit residues: 81.4583 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [111, 42, 108, 18, 3, 92, 15, 80, 54, 65, 9] chunk 111 optimal weight: 6.9990 chunk 42 optimal weight: 0.4980 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.188639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.135799 restraints weight = 9141.790| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.05 r_work: 0.3379 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9284 Z= 0.129 Angle : 0.539 7.331 12590 Z= 0.290 Chirality : 0.042 0.138 1430 Planarity : 0.004 0.057 1588 Dihedral : 5.737 63.655 1274 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.93 % Allowed : 16.16 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.20 (0.24), residues: 1134 helix: 2.72 (0.24), residues: 412 sheet: 0.75 (0.30), residues: 280 loop : -1.10 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.024 0.001 TYR R 92 PHE 0.016 0.001 PHE B 151 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 9280) covalent geometry : angle 0.53641 / 0.29 (12582) SS BOND : bond 0.00514 / 0.31 ( 4) SS BOND : angle 1.98827 / 1.02 ( 8) hydrogen bonds : bond 0.04913 / 3.37 ( 463) hydrogen bonds : angle 4.36388 / 3.05 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 28 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7784 (tp-100) REVERT: A 57 LYS cc_start: 0.6532 (mttp) cc_final: 0.6326 (mttm) REVERT: A 191 GLU cc_start: 0.8444 (tt0) cc_final: 0.8005 (tt0) REVERT: A 196 LEU cc_start: 0.5159 (OUTLIER) cc_final: 0.4738 (tm) REVERT: A 256 ARG cc_start: 0.7067 (ttt90) cc_final: 0.6201 (ttp-170) REVERT: A 316 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7222 (mt) REVERT: A 345 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7033 (mmtt) REVERT: A 350 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: A 354 LYS cc_start: 0.7946 (mttt) cc_final: 0.7283 (mmtt) REVERT: B 23 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7503 (mtmt) REVERT: B 46 ARG cc_start: 0.8114 (mtm180) cc_final: 0.7828 (mtp180) REVERT: B 55 LEU cc_start: 0.8066 (pp) cc_final: 0.7617 (mt) REVERT: B 146 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8442 (mm) REVERT: B 184 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8436 (p) REVERT: B 217 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8170 (pmm) REVERT: B 270 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.7756 (pp) REVERT: B 318 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 338 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (mp) REVERT: D 43 LYS cc_start: 0.7785 (mmtm) cc_final: 0.7062 (mptt) REVERT: D 93 MET cc_start: 0.8503 (ttp) cc_final: 0.7951 (tpp) REVERT: D 113 GLN cc_start: 0.7868 (mt0) cc_final: 0.7398 (mm110) REVERT: D 174 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7887 (pp30) REVERT: R 92 TYR cc_start: 0.6375 (t80) cc_final: 0.6036 (t80) REVERT: R 147 PHE cc_start: 0.6548 (m-80) cc_final: 0.6122 (m-80) REVERT: R 164 MET cc_start: 0.4078 (ptm) cc_final: 0.3081 (mmm) REVERT: R 184 TYR cc_start: 0.5258 (t80) cc_final: 0.4810 (t80) outliers start: 29 outliers final: 19 residues processed: 133 average time/residue: 0.5776 time to fit residues: 81.9740 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [107, 15, 87, 79, 86, 37, 42, 29, 22, 59, 66] chunk 107 optimal weight: 6.9990 chunk 15 optimal weight: 0.0040 chunk 87 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 42 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.4552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.191857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.136298 restraints weight = 9265.647| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.77 r_work: 0.3442 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9284 Z= 0.098 Angle : 0.487 6.859 12590 Z= 0.263 Chirality : 0.041 0.135 1430 Planarity : 0.004 0.056 1588 Dihedral : 5.381 58.405 1274 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.42 % Allowed : 16.87 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.40 (0.25), residues: 1134 helix: 2.90 (0.24), residues: 413 sheet: 0.81 (0.30), residues: 284 loop : -1.01 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.022 0.001 TYR R 92 PHE 0.016 0.001 PHE A 55 TRP 0.015 0.001 TRP B 297 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 ( 9280) covalent geometry : angle 0.48605 / 0.26 (12582) SS BOND : bond 0.00387 / 0.23 ( 4) SS BOND : angle 1.48103 / 0.77 ( 8) hydrogen bonds : bond 0.04131 / 2.83 ( 463) hydrogen bonds : angle 4.14956 / 2.89 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 28 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7837 (tp-100) REVERT: A 57 LYS cc_start: 0.6598 (mttp) cc_final: 0.6393 (mttm) REVERT: A 191 GLU cc_start: 0.8359 (tt0) cc_final: 0.7905 (tt0) REVERT: A 256 ARG cc_start: 0.7025 (ttt90) cc_final: 0.6173 (ttp-170) REVERT: A 316 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7080 (mt) REVERT: A 345 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7033 (mmtt) REVERT: A 350 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: A 354 LYS cc_start: 0.7896 (mttt) cc_final: 0.7223 (mmtt) REVERT: B 23 LYS cc_start: 0.7966 (ttmt) cc_final: 0.7445 (mtmt) REVERT: B 46 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7793 (mtp180) REVERT: B 55 LEU cc_start: 0.8013 (pp) cc_final: 0.7521 (mt) REVERT: B 134 ARG cc_start: 0.8459 (ptt-90) cc_final: 0.7480 (ppt170) REVERT: B 146 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8446 (mm) REVERT: B 172 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7428 (tp30) REVERT: B 184 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 217 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8090 (pmm) REVERT: D 43 LYS cc_start: 0.7652 (mmtm) cc_final: 0.6962 (mttp) REVERT: D 93 MET cc_start: 0.8440 (ttp) cc_final: 0.7956 (tpp) REVERT: D 113 GLN cc_start: 0.7875 (mt0) cc_final: 0.7440 (mm110) REVERT: D 174 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: R 147 PHE cc_start: 0.6651 (m-80) cc_final: 0.6233 (m-80) REVERT: R 164 MET cc_start: 0.4052 (ptm) cc_final: 0.3034 (mmm) REVERT: R 184 TYR cc_start: 0.5331 (t80) cc_final: 0.4823 (t80) outliers start: 24 outliers final: 14 residues processed: 137 average time/residue: 0.5736 time to fit residues: 83.8729 Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: [109, 33, 7, 65, 48, 17, 12, 74, 44, 45, 27] chunk 109 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN D 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.189378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133277 restraints weight = 9049.150| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.74 r_work: 0.3408 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9284 Z= 0.128 Angle : 0.539 8.100 12590 Z= 0.288 Chirality : 0.042 0.147 1430 Planarity : 0.004 0.061 1588 Dihedral : 5.558 62.867 1273 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.53 % Allowed : 16.77 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.31 (0.24), residues: 1134 helix: 2.84 (0.24), residues: 412 sheet: 0.77 (0.30), residues: 280 loop : -1.06 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 19 TYR 0.009 0.001 TYR D 178 PHE 0.022 0.001 PHE R 150 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9280) covalent geometry : angle 0.53719 / 0.29 (12582) SS BOND : bond 0.00543 / 0.33 ( 4) SS BOND : angle 1.87686 / 0.93 ( 8) hydrogen bonds : bond 0.04741 / 3.25 ( 463) hydrogen bonds : angle 4.28184 / 2.99 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.42 seconds wall clock time: 73 minutes 1.56 seconds (4381.56 seconds total)