Starting phenix.real_space_refine on Wed Sep 17 13:02:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y51_38927/09_2025/8y51_38927.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y51_38927/09_2025/8y51_38927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y51_38927/09_2025/8y51_38927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y51_38927/09_2025/8y51_38927.map" model { file = "/net/cci-nas-00/data/ceres_data/8y51_38927/09_2025/8y51_38927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y51_38927/09_2025/8y51_38927.cif" } resolution = 3.3 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= 0.003 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 54 5.16 5 C 5658 2.51 5 N 1522 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8883 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2592 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2208 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 2 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Time building chain proxies: 1.95, per 1000 atoms: 0.22 Number of scatterers: 8883 At special positions: 0 Unit cell: (120.96, 88.56, 129.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1649 8.00 N 1522 7.00 C 5658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.71 Conformation dependent library (CDL) restraints added in 464.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 40.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.515A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 229 through 245 removed outlier: 3.957A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.795A pdb=" N ILE A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.550A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 3.581A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 44 removed outlier: 3.506A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 49 through 75 removed outlier: 3.989A pdb=" N THR R 53 " --> pdb=" O ALA R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 79 Processing helix chain 'R' and resid 80 through 108 removed outlier: 3.594A pdb=" N ILE R 84 " --> pdb=" O THR R 80 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE R 85 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE R 86 " --> pdb=" O PRO R 82 " (cutoff:3.500A) Proline residue: R 102 - end of helix removed outlier: 3.583A pdb=" N ALA R 105 " --> pdb=" O VAL R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 150 Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 160 through 180 removed outlier: 3.698A pdb=" N THR R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 183 No H-bonds generated for 'chain 'R' and resid 181 through 183' Processing helix chain 'R' and resid 212 through 247 Proline residue: R 229 - end of helix Processing helix chain 'R' and resid 256 through 294 removed outlier: 3.614A pdb=" N LEU R 274 " --> pdb=" O ALA R 270 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS R 283 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 286 - end of helix Processing helix chain 'R' and resid 305 through 334 removed outlier: 3.567A pdb=" N PHE R 309 " --> pdb=" O SER R 305 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE R 310 " --> pdb=" O ALA R 306 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN R 322 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER R 323 " --> pdb=" O ALA R 319 " (cutoff:3.500A) Proline residue: R 327 - end of helix removed outlier: 3.726A pdb=" N LEU R 330 " --> pdb=" O ASN R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 349 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.680A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.522A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.786A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.823A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.966A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.708A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 76 " --> pdb=" O HIS B 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 77 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.636A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 119 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 127 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.779A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.450A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 206 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 214 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.513A pdb=" N ARG B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP B 259 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.854A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 294 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 299 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL B 312 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 301 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.453A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.759A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1236 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: 1.53 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1473 1.32 - 1.44: 2461 1.44 - 1.57: 5055 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 9064 Sorted by residual: bond pdb=" C LYS R 167 " pdb=" O LYS R 167 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.19e-02 7.06e+03 9.71e+00 bond pdb=" N ALA R 110 " pdb=" CA ALA R 110 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.28e+00 bond pdb=" N GLU B 8 " pdb=" CA GLU B 8 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N THR G 5 " pdb=" CA THR G 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N LEU A 5 " pdb=" CA LEU A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 ... (remaining 9059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 12101 1.34 - 2.69: 129 2.69 - 4.03: 38 4.03 - 5.37: 2 5.37 - 6.72: 3 Bond angle restraints: 12273 Sorted by residual: angle pdb=" N GLY R 112 " pdb=" CA GLY R 112 " pdb=" C GLY R 112 " ideal model delta sigma weight residual 112.45 119.17 -6.72 1.55e+00 4.16e-01 1.88e+01 angle pdb=" CB LYS R 167 " pdb=" CG LYS R 167 " pdb=" CD LYS R 167 " ideal model delta sigma weight residual 111.30 117.71 -6.41 2.30e+00 1.89e-01 7.77e+00 angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 113.10 110.40 2.70 9.70e-01 1.06e+00 7.76e+00 angle pdb=" N ALA R 110 " pdb=" CA ALA R 110 " pdb=" C ALA R 110 " ideal model delta sigma weight residual 110.80 116.58 -5.78 2.13e+00 2.20e-01 7.37e+00 angle pdb=" N ILE R 228 " pdb=" CA ILE R 228 " pdb=" C ILE R 228 " ideal model delta sigma weight residual 112.35 109.26 3.09 1.20e+00 6.94e-01 6.62e+00 ... (remaining 12268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 5237 17.00 - 34.00: 124 34.00 - 51.00: 23 51.00 - 68.00: 7 68.00 - 84.99: 3 Dihedral angle restraints: 5394 sinusoidal: 2106 harmonic: 3288 Sorted by residual: dihedral pdb=" N PHE R 225 " pdb=" CA PHE R 225 " pdb=" CB PHE R 225 " pdb=" CG PHE R 225 " ideal model delta sinusoidal sigma weight residual 60.00 118.75 -58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE B 239 " pdb=" CA PHE B 239 " pdb=" CB PHE B 239 " pdb=" CG PHE B 239 " ideal model delta sinusoidal sigma weight residual -180.00 -124.76 -55.24 3 1.50e+01 4.44e-03 9.33e+00 dihedral pdb=" N ARG E 191 " pdb=" CA ARG E 191 " pdb=" CB ARG E 191 " pdb=" CG ARG E 191 " ideal model delta sinusoidal sigma weight residual -60.00 -111.52 51.52 3 1.50e+01 4.44e-03 9.02e+00 ... (remaining 5391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1100 0.036 - 0.073: 198 0.073 - 0.109: 65 0.109 - 0.145: 36 0.145 - 0.182: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA ALA R 110 " pdb=" N ALA R 110 " pdb=" C ALA R 110 " pdb=" CB ALA R 110 " both_signs ideal model delta sigma weight residual False 2.48 2.30 0.18 2.00e-01 2.50e+01 8.26e-01 chirality pdb=" CA ILE B 237 " pdb=" N ILE B 237 " pdb=" C ILE B 237 " pdb=" CB ILE B 237 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE R 251 " pdb=" N ILE R 251 " pdb=" C ILE R 251 " pdb=" CB ILE R 251 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1397 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO E 236 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 251 " 0.015 5.00e-02 4.00e+02 2.29e-02 8.37e-01 pdb=" N PRO R 252 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO R 252 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO R 252 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 109 " -0.004 2.00e-02 2.50e+03 8.51e-03 7.25e-01 pdb=" C LEU R 109 " 0.015 2.00e-02 2.50e+03 pdb=" O LEU R 109 " -0.005 2.00e-02 2.50e+03 pdb=" N ALA R 110 " -0.005 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 121 2.62 - 3.19: 8291 3.19 - 3.76: 13624 3.76 - 4.33: 18993 4.33 - 4.90: 31923 Nonbonded interactions: 72952 Sorted by model distance: nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.053 3.040 nonbonded pdb=" O LEU R 318 " pdb=" OG SER R 321 " model vdw 2.106 3.040 nonbonded pdb=" OG SER G 56 " pdb=" OE1 GLU G 57 " model vdw 2.124 3.040 nonbonded pdb=" CG2 THR R 80 " pdb=" OD1 ASN R 83 " model vdw 2.134 3.460 nonbonded pdb=" OE2 GLU A 207 " pdb=" NH1 ARG A 209 " model vdw 2.163 3.120 ... (remaining 72947 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.720 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9064 Z= 0.116 Angle : 0.426 6.718 12273 Z= 0.263 Chirality : 0.038 0.182 1400 Planarity : 0.002 0.051 1548 Dihedral : 8.227 84.994 3268 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 0.81 % Favored : 99.10 % Rotamer: Outliers : 0.21 % Allowed : 1.95 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.23), residues: 1110 helix: 0.74 (0.24), residues: 393 sheet: -1.04 (0.29), residues: 285 loop : -1.50 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 15 TYR 0.005 0.001 TYR E 235 PHE 0.007 0.001 PHE R 115 TRP 0.003 0.000 TRP A 211 HIS 0.002 0.000 HIS R 294 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 9064) covalent geometry : angle 0.42572 (12273) hydrogen bonds : bond 0.16321 ( 438) hydrogen bonds : angle 6.29294 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 GLN cc_start: 0.6767 (tt0) cc_final: 0.6246 (tt0) REVERT: B 294 TYR cc_start: 0.8107 (m-80) cc_final: 0.7754 (m-80) REVERT: G 39 TYR cc_start: 0.6502 (t80) cc_final: 0.6268 (t80) REVERT: E 18 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7773 (ttmm) outliers start: 2 outliers final: 1 residues processed: 316 average time/residue: 0.1223 time to fit residues: 50.1336 Evaluate side-chains 186 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 67 HIS B 235 ASN B 271 HIS B 300 ASN E 76 ASN E 183 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.086943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.067210 restraints weight = 26195.565| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.10 r_work: 0.3075 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9064 Z= 0.143 Angle : 0.616 7.308 12273 Z= 0.318 Chirality : 0.042 0.170 1400 Planarity : 0.005 0.056 1548 Dihedral : 3.829 57.376 1228 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.39 % Allowed : 11.41 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.25), residues: 1110 helix: 1.61 (0.26), residues: 391 sheet: -0.45 (0.30), residues: 269 loop : -0.61 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 160 TYR 0.022 0.002 TYR A 278 PHE 0.011 0.001 PHE R 337 TRP 0.016 0.001 TRP B 174 HIS 0.007 0.001 HIS R 217 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9064) covalent geometry : angle 0.61593 (12273) hydrogen bonds : bond 0.03398 ( 438) hydrogen bonds : angle 4.64338 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8919 (m-30) cc_final: 0.8652 (m-30) REVERT: A 356 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8748 (ttm110) REVERT: B 37 GLN cc_start: 0.9459 (mt0) cc_final: 0.9232 (mp10) REVERT: B 129 TYR cc_start: 0.8864 (m-80) cc_final: 0.8568 (m-80) REVERT: B 135 GLU cc_start: 0.8100 (mp0) cc_final: 0.7847 (mp0) REVERT: B 220 GLU cc_start: 0.8501 (mp0) cc_final: 0.8127 (mp0) REVERT: B 264 GLN cc_start: 0.8411 (tt0) cc_final: 0.8129 (tt0) REVERT: B 267 MET cc_start: 0.8035 (tpp) cc_final: 0.7475 (mtp) REVERT: B 285 LYS cc_start: 0.8915 (mtpp) cc_final: 0.8691 (mtpp) REVERT: B 294 TYR cc_start: 0.8650 (m-80) cc_final: 0.8011 (m-80) REVERT: G 37 MET cc_start: 0.8834 (ttp) cc_final: 0.8258 (ttp) REVERT: G 41 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8564 (mm-30) REVERT: R 97 LEU cc_start: 0.9594 (mt) cc_final: 0.9364 (mt) REVERT: R 155 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7985 (ptm-80) REVERT: R 337 PHE cc_start: 0.8976 (t80) cc_final: 0.8774 (t80) REVERT: E 18 LYS cc_start: 0.9444 (ttpt) cc_final: 0.8871 (ttmm) REVERT: E 153 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7821 (tm-30) REVERT: E 186 GLN cc_start: 0.8647 (tt0) cc_final: 0.8346 (tt0) REVERT: E 223 ASP cc_start: 0.7743 (m-30) cc_final: 0.7213 (m-30) outliers start: 33 outliers final: 19 residues processed: 214 average time/residue: 0.1061 time to fit residues: 30.4162 Evaluate side-chains 183 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 231 SER Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN E 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.084715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.064795 restraints weight = 26311.994| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.10 r_work: 0.3020 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9064 Z= 0.141 Angle : 0.576 7.240 12273 Z= 0.299 Chirality : 0.041 0.180 1400 Planarity : 0.004 0.045 1548 Dihedral : 3.931 56.467 1228 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.88 % Allowed : 12.85 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1110 helix: 1.78 (0.26), residues: 394 sheet: -0.24 (0.31), residues: 274 loop : -0.18 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 160 TYR 0.025 0.001 TYR E 235 PHE 0.014 0.001 PHE R 85 TRP 0.013 0.001 TRP B 174 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9064) covalent geometry : angle 0.57638 (12273) hydrogen bonds : bond 0.03241 ( 438) hydrogen bonds : angle 4.46781 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8897 (m-30) cc_final: 0.8413 (m-30) REVERT: A 356 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8767 (ttm110) REVERT: B 37 GLN cc_start: 0.9430 (mt0) cc_final: 0.9190 (mp10) REVERT: B 267 MET cc_start: 0.8212 (tpp) cc_final: 0.7767 (mtp) REVERT: B 280 SER cc_start: 0.9083 (t) cc_final: 0.8880 (m) REVERT: B 285 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8754 (mtpp) REVERT: B 294 TYR cc_start: 0.8697 (m-80) cc_final: 0.7714 (m-80) REVERT: B 344 TRP cc_start: 0.8548 (m100) cc_final: 0.8128 (m-10) REVERT: R 78 MET cc_start: 0.8428 (mmm) cc_final: 0.8192 (mmm) REVERT: R 155 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7995 (ptm-80) REVERT: R 337 PHE cc_start: 0.9014 (t80) cc_final: 0.8703 (t80) REVERT: E 18 LYS cc_start: 0.9468 (ttpt) cc_final: 0.8987 (ttmm) REVERT: E 67 PHE cc_start: 0.8700 (m-10) cc_final: 0.8161 (m-10) REVERT: E 82 MET cc_start: 0.9210 (mmm) cc_final: 0.8555 (mmm) REVERT: E 137 ASP cc_start: 0.8804 (p0) cc_final: 0.8529 (p0) REVERT: E 140 MET cc_start: 0.8440 (mmm) cc_final: 0.7632 (mmm) REVERT: E 153 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7787 (tm-30) REVERT: E 186 GLN cc_start: 0.8742 (tt0) cc_final: 0.8425 (tt0) REVERT: E 218 ARG cc_start: 0.8742 (mtm110) cc_final: 0.8530 (mtm110) outliers start: 28 outliers final: 17 residues processed: 196 average time/residue: 0.1059 time to fit residues: 27.9883 Evaluate side-chains 175 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 231 SER Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN R 294 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.080752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.060383 restraints weight = 26810.717| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.07 r_work: 0.2909 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9064 Z= 0.183 Angle : 0.596 8.195 12273 Z= 0.310 Chirality : 0.042 0.183 1400 Planarity : 0.004 0.053 1548 Dihedral : 4.191 55.821 1228 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.49 % Allowed : 13.26 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.25), residues: 1110 helix: 1.87 (0.26), residues: 394 sheet: 0.00 (0.31), residues: 270 loop : -0.17 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 160 TYR 0.027 0.002 TYR E 235 PHE 0.013 0.001 PHE R 85 TRP 0.014 0.001 TRP B 174 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9064) covalent geometry : angle 0.59613 (12273) hydrogen bonds : bond 0.03290 ( 438) hydrogen bonds : angle 4.35691 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9048 (m-30) cc_final: 0.8835 (m-30) REVERT: B 27 ARG cc_start: 0.8959 (ttm170) cc_final: 0.8631 (mtt180) REVERT: B 37 GLN cc_start: 0.9393 (mt0) cc_final: 0.9144 (mp10) REVERT: B 220 GLU cc_start: 0.8756 (mp0) cc_final: 0.8243 (pm20) REVERT: B 222 MET cc_start: 0.8159 (ppp) cc_final: 0.7689 (ppp) REVERT: B 264 GLN cc_start: 0.8511 (tt0) cc_final: 0.8300 (mt0) REVERT: B 267 MET cc_start: 0.8428 (tpp) cc_final: 0.7970 (mtp) REVERT: B 280 SER cc_start: 0.9223 (t) cc_final: 0.8949 (m) REVERT: B 285 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8751 (mtpp) REVERT: R 93 ASP cc_start: 0.8593 (m-30) cc_final: 0.8158 (t0) REVERT: R 155 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8102 (ptm-80) REVERT: R 254 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7911 (mp0) REVERT: R 337 PHE cc_start: 0.9068 (t80) cc_final: 0.8760 (t80) REVERT: E 18 LYS cc_start: 0.9489 (ttpt) cc_final: 0.8998 (ttmm) REVERT: E 82 MET cc_start: 0.9239 (mmm) cc_final: 0.8814 (mmm) REVERT: E 137 ASP cc_start: 0.8803 (p0) cc_final: 0.8540 (p0) REVERT: E 140 MET cc_start: 0.8358 (mmm) cc_final: 0.7852 (mmm) REVERT: E 153 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7956 (tm-30) REVERT: E 186 GLN cc_start: 0.8829 (tt0) cc_final: 0.8545 (tt0) REVERT: E 218 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8509 (mtm110) outliers start: 34 outliers final: 24 residues processed: 185 average time/residue: 0.1077 time to fit residues: 26.8821 Evaluate side-chains 171 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 231 SER Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 23 optimal weight: 0.0770 chunk 76 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 72 optimal weight: 0.0370 chunk 8 optimal weight: 4.9990 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.063267 restraints weight = 26491.659| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.06 r_work: 0.2976 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9064 Z= 0.104 Angle : 0.553 8.858 12273 Z= 0.286 Chirality : 0.040 0.162 1400 Planarity : 0.004 0.051 1548 Dihedral : 3.946 55.160 1228 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.16 % Allowed : 15.72 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.25), residues: 1110 helix: 2.10 (0.26), residues: 394 sheet: 0.11 (0.32), residues: 258 loop : -0.08 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 160 TYR 0.020 0.001 TYR E 235 PHE 0.018 0.001 PHE R 222 TRP 0.014 0.001 TRP B 174 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9064) covalent geometry : angle 0.55287 (12273) hydrogen bonds : bond 0.02969 ( 438) hydrogen bonds : angle 4.23846 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9000 (m-30) cc_final: 0.8797 (m-30) REVERT: B 27 ARG cc_start: 0.9034 (ttm170) cc_final: 0.8430 (ttt180) REVERT: B 37 GLN cc_start: 0.9383 (mt0) cc_final: 0.9157 (mp10) REVERT: B 135 GLU cc_start: 0.8617 (mp0) cc_final: 0.8233 (mp0) REVERT: B 220 GLU cc_start: 0.8824 (mp0) cc_final: 0.8594 (pm20) REVERT: B 264 GLN cc_start: 0.8374 (tt0) cc_final: 0.8113 (mt0) REVERT: B 267 MET cc_start: 0.8321 (tpp) cc_final: 0.7984 (mtp) REVERT: B 280 SER cc_start: 0.9196 (t) cc_final: 0.8995 (m) REVERT: B 285 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8733 (mtpp) REVERT: B 294 TYR cc_start: 0.8875 (m-80) cc_final: 0.8580 (m-80) REVERT: G 28 LYS cc_start: 0.8619 (tppt) cc_final: 0.8325 (tptm) REVERT: R 154 GLU cc_start: 0.8302 (mp0) cc_final: 0.7876 (mp0) REVERT: R 254 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7657 (mp0) REVERT: R 255 GLU cc_start: 0.8602 (tp30) cc_final: 0.8399 (tm-30) REVERT: R 337 PHE cc_start: 0.8996 (t80) cc_final: 0.8619 (t80) REVERT: E 18 LYS cc_start: 0.9461 (ttpt) cc_final: 0.9157 (ttmm) REVERT: E 82 MET cc_start: 0.9156 (mmm) cc_final: 0.8745 (mmm) REVERT: E 108 ASP cc_start: 0.9099 (p0) cc_final: 0.8705 (p0) REVERT: E 137 ASP cc_start: 0.8810 (p0) cc_final: 0.8553 (p0) REVERT: E 153 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7965 (tm-30) REVERT: E 186 GLN cc_start: 0.8806 (tt0) cc_final: 0.8592 (tt0) REVERT: E 218 ARG cc_start: 0.8967 (mtm110) cc_final: 0.8747 (mtm110) REVERT: E 220 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8495 (mm-30) REVERT: E 230 MET cc_start: 0.9044 (ttp) cc_final: 0.8659 (tmm) outliers start: 21 outliers final: 14 residues processed: 178 average time/residue: 0.1109 time to fit residues: 26.3293 Evaluate side-chains 161 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.079802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059618 restraints weight = 26626.442| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 4.00 r_work: 0.2884 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9064 Z= 0.179 Angle : 0.620 10.753 12273 Z= 0.314 Chirality : 0.041 0.178 1400 Planarity : 0.004 0.053 1548 Dihedral : 4.101 55.066 1228 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.98 % Allowed : 15.83 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1110 helix: 2.20 (0.26), residues: 394 sheet: 0.11 (0.31), residues: 279 loop : 0.06 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.028 0.001 TYR E 235 PHE 0.012 0.001 PHE R 85 TRP 0.016 0.001 TRP B 174 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9064) covalent geometry : angle 0.61993 (12273) hydrogen bonds : bond 0.03191 ( 438) hydrogen bonds : angle 4.29313 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9095 (m-30) cc_final: 0.8856 (m-30) REVERT: B 27 ARG cc_start: 0.9044 (ttm170) cc_final: 0.8417 (ttt180) REVERT: B 37 GLN cc_start: 0.9386 (mt0) cc_final: 0.9136 (mp10) REVERT: B 135 GLU cc_start: 0.8703 (mp0) cc_final: 0.8417 (mp0) REVERT: B 220 GLU cc_start: 0.8739 (mp0) cc_final: 0.8293 (pm20) REVERT: B 228 THR cc_start: 0.8791 (p) cc_final: 0.8506 (t) REVERT: B 264 GLN cc_start: 0.8378 (tt0) cc_final: 0.8065 (mt0) REVERT: B 267 MET cc_start: 0.8459 (tpp) cc_final: 0.7988 (mtt) REVERT: B 280 SER cc_start: 0.9279 (t) cc_final: 0.8957 (m) REVERT: B 285 LYS cc_start: 0.9140 (mtpp) cc_final: 0.8774 (mtpp) REVERT: B 306 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8490 (mmmt) REVERT: G 19 LYS cc_start: 0.9653 (ptpt) cc_final: 0.9449 (ptpp) REVERT: G 37 MET cc_start: 0.8816 (ttp) cc_final: 0.8081 (tmm) REVERT: R 93 ASP cc_start: 0.8399 (m-30) cc_final: 0.8065 (t0) REVERT: R 154 GLU cc_start: 0.8337 (mp0) cc_final: 0.7872 (mp0) REVERT: R 254 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7843 (mp0) REVERT: R 337 PHE cc_start: 0.9055 (t80) cc_final: 0.8667 (t80) REVERT: E 18 LYS cc_start: 0.9462 (ttpt) cc_final: 0.9007 (ttmm) REVERT: E 82 MET cc_start: 0.9255 (mmm) cc_final: 0.8948 (mmm) REVERT: E 137 ASP cc_start: 0.8769 (p0) cc_final: 0.8507 (p0) REVERT: E 153 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7932 (tm-30) REVERT: E 186 GLN cc_start: 0.8856 (tt0) cc_final: 0.8639 (tt0) REVERT: E 218 ARG cc_start: 0.8959 (mtm110) cc_final: 0.8315 (mtm110) REVERT: E 220 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8159 (mp0) REVERT: E 230 MET cc_start: 0.9071 (ttp) cc_final: 0.8738 (tmm) outliers start: 29 outliers final: 22 residues processed: 174 average time/residue: 0.1169 time to fit residues: 27.0198 Evaluate side-chains 170 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.058685 restraints weight = 26714.072| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.00 r_work: 0.2866 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9064 Z= 0.173 Angle : 0.625 11.340 12273 Z= 0.316 Chirality : 0.041 0.178 1400 Planarity : 0.004 0.051 1548 Dihedral : 4.208 54.970 1228 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.19 % Allowed : 16.24 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.26), residues: 1110 helix: 2.20 (0.26), residues: 394 sheet: 0.16 (0.32), residues: 279 loop : 0.12 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 284 TYR 0.028 0.001 TYR E 235 PHE 0.011 0.001 PHE A 189 TRP 0.014 0.001 TRP B 174 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9064) covalent geometry : angle 0.62492 (12273) hydrogen bonds : bond 0.03235 ( 438) hydrogen bonds : angle 4.32272 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.9137 (m-30) cc_final: 0.8887 (m-30) REVERT: A 209 ARG cc_start: 0.8686 (ptt-90) cc_final: 0.8202 (ttp-110) REVERT: B 27 ARG cc_start: 0.9023 (ttm170) cc_final: 0.8454 (ttt180) REVERT: B 135 GLU cc_start: 0.8747 (mp0) cc_final: 0.8503 (mp0) REVERT: B 177 GLU cc_start: 0.9102 (mp0) cc_final: 0.8809 (pm20) REVERT: B 220 GLU cc_start: 0.8757 (mp0) cc_final: 0.8518 (pm20) REVERT: B 228 THR cc_start: 0.8737 (p) cc_final: 0.8419 (t) REVERT: B 239 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8705 (m-80) REVERT: B 264 GLN cc_start: 0.8326 (tt0) cc_final: 0.7986 (mt0) REVERT: B 280 SER cc_start: 0.9319 (t) cc_final: 0.8961 (m) REVERT: B 285 LYS cc_start: 0.9156 (mtpp) cc_final: 0.8628 (ttmm) REVERT: B 306 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8604 (mmmt) REVERT: G 16 GLU cc_start: 0.9596 (tp30) cc_final: 0.9257 (tp30) REVERT: G 20 MET cc_start: 0.9368 (mmm) cc_final: 0.8964 (mmm) REVERT: G 37 MET cc_start: 0.8856 (ttp) cc_final: 0.8236 (tmm) REVERT: R 93 ASP cc_start: 0.8431 (m-30) cc_final: 0.8086 (t0) REVERT: R 154 GLU cc_start: 0.8403 (mp0) cc_final: 0.7973 (mp0) REVERT: R 337 PHE cc_start: 0.9061 (t80) cc_final: 0.8682 (t80) REVERT: E 18 LYS cc_start: 0.9486 (ttpt) cc_final: 0.9013 (ttmm) REVERT: E 82 MET cc_start: 0.9232 (mmm) cc_final: 0.8893 (mmm) REVERT: E 108 ASP cc_start: 0.9088 (p0) cc_final: 0.8863 (p0) REVERT: E 116 LEU cc_start: 0.9253 (tp) cc_final: 0.8988 (tt) REVERT: E 137 ASP cc_start: 0.8784 (p0) cc_final: 0.8538 (p0) REVERT: E 153 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7951 (tm-30) REVERT: E 186 GLN cc_start: 0.8857 (tt0) cc_final: 0.8644 (tt0) REVERT: E 218 ARG cc_start: 0.9019 (mtm110) cc_final: 0.8749 (mtm110) REVERT: E 220 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8582 (mm-30) REVERT: E 230 MET cc_start: 0.9086 (ttp) cc_final: 0.8831 (tmm) outliers start: 31 outliers final: 21 residues processed: 178 average time/residue: 0.1160 time to fit residues: 27.5172 Evaluate side-chains 169 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain R residue 323 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 245 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN ** R 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057039 restraints weight = 26678.647| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.97 r_work: 0.2827 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9064 Z= 0.210 Angle : 0.667 12.225 12273 Z= 0.335 Chirality : 0.042 0.173 1400 Planarity : 0.004 0.050 1548 Dihedral : 4.370 55.068 1228 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.29 % Allowed : 16.65 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.26), residues: 1110 helix: 2.13 (0.26), residues: 396 sheet: 0.45 (0.33), residues: 260 loop : 0.06 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 160 TYR 0.035 0.001 TYR E 235 PHE 0.012 0.001 PHE R 85 TRP 0.013 0.001 TRP B 174 HIS 0.005 0.001 HIS R 217 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9064) covalent geometry : angle 0.66695 (12273) hydrogen bonds : bond 0.03310 ( 438) hydrogen bonds : angle 4.41735 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8999 (pp30) REVERT: B 27 ARG cc_start: 0.9028 (ttm170) cc_final: 0.8554 (ttt180) REVERT: B 228 THR cc_start: 0.8752 (p) cc_final: 0.8365 (t) REVERT: B 239 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: B 264 GLN cc_start: 0.8405 (tt0) cc_final: 0.8058 (mt0) REVERT: B 267 MET cc_start: 0.8501 (tpp) cc_final: 0.8104 (mtt) REVERT: B 280 SER cc_start: 0.9261 (t) cc_final: 0.8908 (m) REVERT: B 285 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8951 (mtpp) REVERT: G 16 GLU cc_start: 0.9621 (tp30) cc_final: 0.9183 (tp30) REVERT: G 20 MET cc_start: 0.9425 (mmm) cc_final: 0.9007 (mmm) REVERT: R 93 ASP cc_start: 0.8445 (m-30) cc_final: 0.8080 (t0) REVERT: R 154 GLU cc_start: 0.8499 (mp0) cc_final: 0.8043 (mp0) REVERT: R 337 PHE cc_start: 0.9098 (t80) cc_final: 0.8751 (t80) REVERT: E 18 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9251 (ttmm) REVERT: E 72 ASP cc_start: 0.7685 (t70) cc_final: 0.7233 (t70) REVERT: E 82 MET cc_start: 0.9206 (mmm) cc_final: 0.8750 (mmm) REVERT: E 116 LEU cc_start: 0.9265 (tp) cc_final: 0.8986 (tt) REVERT: E 137 ASP cc_start: 0.8790 (p0) cc_final: 0.8547 (p0) REVERT: E 153 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7951 (tm-30) REVERT: E 186 GLN cc_start: 0.8891 (tt0) cc_final: 0.8679 (tt0) REVERT: E 218 ARG cc_start: 0.8985 (mtm110) cc_final: 0.8710 (mtm110) REVERT: E 220 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8577 (mm-30) REVERT: E 230 MET cc_start: 0.9066 (ttp) cc_final: 0.8843 (tmm) outliers start: 32 outliers final: 22 residues processed: 176 average time/residue: 0.1141 time to fit residues: 26.7037 Evaluate side-chains 174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056739 restraints weight = 26381.680| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.88 r_work: 0.2821 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9064 Z= 0.222 Angle : 0.733 11.901 12273 Z= 0.363 Chirality : 0.043 0.216 1400 Planarity : 0.004 0.060 1548 Dihedral : 4.479 54.918 1228 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.57 % Allowed : 17.99 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.26), residues: 1110 helix: 1.98 (0.25), residues: 397 sheet: 0.39 (0.33), residues: 259 loop : 0.03 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 160 TYR 0.043 0.002 TYR E 235 PHE 0.012 0.002 PHE R 85 TRP 0.015 0.001 TRP B 174 HIS 0.005 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9064) covalent geometry : angle 0.73276 (12273) hydrogen bonds : bond 0.03383 ( 438) hydrogen bonds : angle 4.48710 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8872 (mmm) cc_final: 0.8655 (mmm) REVERT: B 27 ARG cc_start: 0.8982 (ttm170) cc_final: 0.8500 (ttt180) REVERT: B 50 MET cc_start: 0.8985 (mmt) cc_final: 0.8781 (mmm) REVERT: B 222 MET cc_start: 0.8633 (ppp) cc_final: 0.8363 (pmm) REVERT: B 239 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: B 264 GLN cc_start: 0.8420 (tt0) cc_final: 0.8072 (mt0) REVERT: B 280 SER cc_start: 0.9296 (t) cc_final: 0.8932 (m) REVERT: B 285 LYS cc_start: 0.9151 (mtpp) cc_final: 0.8945 (mtpp) REVERT: G 20 MET cc_start: 0.9424 (mmm) cc_final: 0.9188 (tpp) REVERT: R 93 ASP cc_start: 0.8435 (m-30) cc_final: 0.8068 (t0) REVERT: R 154 GLU cc_start: 0.8493 (mp0) cc_final: 0.8041 (mp0) REVERT: R 254 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7621 (mp0) REVERT: R 337 PHE cc_start: 0.9122 (t80) cc_final: 0.8758 (t80) REVERT: E 82 MET cc_start: 0.9168 (mmm) cc_final: 0.8798 (mmm) REVERT: E 116 LEU cc_start: 0.9309 (tp) cc_final: 0.9037 (tt) REVERT: E 137 ASP cc_start: 0.8775 (p0) cc_final: 0.8539 (p0) REVERT: E 153 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7969 (tm-30) REVERT: E 186 GLN cc_start: 0.8886 (tt0) cc_final: 0.8680 (tt0) REVERT: E 218 ARG cc_start: 0.8968 (mtm110) cc_final: 0.8682 (mtm110) REVERT: E 220 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8564 (mm-30) REVERT: E 230 MET cc_start: 0.9068 (ttp) cc_final: 0.8860 (tmm) outliers start: 25 outliers final: 23 residues processed: 172 average time/residue: 0.1091 time to fit residues: 25.2705 Evaluate side-chains 168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 101 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056766 restraints weight = 26702.487| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.91 r_work: 0.2823 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9064 Z= 0.201 Angle : 0.760 15.161 12273 Z= 0.375 Chirality : 0.043 0.282 1400 Planarity : 0.004 0.063 1548 Dihedral : 4.522 54.674 1228 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.98 % Allowed : 17.78 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1110 helix: 1.97 (0.26), residues: 396 sheet: 0.39 (0.34), residues: 259 loop : 0.03 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 160 TYR 0.043 0.002 TYR E 235 PHE 0.028 0.002 PHE R 222 TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 9064) covalent geometry : angle 0.75992 (12273) hydrogen bonds : bond 0.03460 ( 438) hydrogen bonds : angle 4.46055 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8832 (mmm) cc_final: 0.8607 (mmm) REVERT: A 284 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8928 (ptm-80) REVERT: B 22 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9169 (pp30) REVERT: B 27 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8458 (ttt180) REVERT: B 135 GLU cc_start: 0.8824 (mp0) cc_final: 0.8622 (mp0) REVERT: B 222 MET cc_start: 0.8662 (ppp) cc_final: 0.8357 (pmm) REVERT: B 239 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8461 (m-80) REVERT: B 264 GLN cc_start: 0.8367 (tt0) cc_final: 0.8024 (mt0) REVERT: B 280 SER cc_start: 0.9330 (t) cc_final: 0.8979 (m) REVERT: B 285 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8614 (ttmm) REVERT: G 26 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7969 (tpp80) REVERT: R 93 ASP cc_start: 0.8423 (m-30) cc_final: 0.8054 (t0) REVERT: R 154 GLU cc_start: 0.8509 (mp0) cc_final: 0.8054 (mp0) REVERT: R 337 PHE cc_start: 0.9098 (t80) cc_final: 0.8731 (t80) REVERT: E 82 MET cc_start: 0.9139 (mmm) cc_final: 0.8746 (mmm) REVERT: E 92 MET cc_start: 0.9167 (tpp) cc_final: 0.8716 (tpp) REVERT: E 116 LEU cc_start: 0.9309 (tp) cc_final: 0.9043 (tt) REVERT: E 137 ASP cc_start: 0.8765 (p0) cc_final: 0.8536 (p0) REVERT: E 153 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8016 (tm-30) REVERT: E 186 GLN cc_start: 0.8892 (tt0) cc_final: 0.8688 (tt0) REVERT: E 218 ARG cc_start: 0.8961 (mtm110) cc_final: 0.8678 (mtm110) REVERT: E 220 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8575 (mm-30) REVERT: E 230 MET cc_start: 0.9079 (ttp) cc_final: 0.8872 (tmm) outliers start: 29 outliers final: 25 residues processed: 171 average time/residue: 0.1131 time to fit residues: 25.9158 Evaluate side-chains 171 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 171 VAL Chi-restraints excluded: chain R residue 221 CYS Chi-restraints excluded: chain R residue 225 PHE Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 314 PHE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 101 optimal weight: 0.0970 chunk 48 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 261 GLN ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.079347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059392 restraints weight = 26184.701| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.93 r_work: 0.2892 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9064 Z= 0.137 Angle : 0.745 13.316 12273 Z= 0.371 Chirality : 0.042 0.264 1400 Planarity : 0.004 0.062 1548 Dihedral : 4.425 53.983 1228 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.06 % Allowed : 18.91 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1110 helix: 2.00 (0.26), residues: 395 sheet: 0.46 (0.34), residues: 255 loop : -0.02 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 160 TYR 0.038 0.001 TYR E 235 PHE 0.024 0.001 PHE A 189 TRP 0.010 0.001 TRP B 174 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9064) covalent geometry : angle 0.74488 (12273) hydrogen bonds : bond 0.03250 ( 438) hydrogen bonds : angle 4.40516 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2657.88 seconds wall clock time: 46 minutes 25.76 seconds (2785.76 seconds total)