Starting phenix.real_space_refine on Fri Nov 15 11:34:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/11_2024/8j21_35941.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/11_2024/8j21_35941.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/11_2024/8j21_35941.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/11_2024/8j21_35941.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/11_2024/8j21_35941.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j21_35941/11_2024/8j21_35941.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 58 5.16 5 C 5612 2.51 5 N 1495 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1775 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2188 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BUA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.63 Number of scatterers: 8803 At special positions: 0 Unit cell: (114.4, 109.2, 121.68, 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 58 16.00 O 1638 8.00 N 1495 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 169 " distance=2.04 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: 2.43 Conformation dependent library (CDL) restraints added in 961.2 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 38.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.371A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.510A pdb=" N ILE A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.761A pdb=" N SER B 69 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.919A pdb=" N GLY B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.665A pdb=" N THR B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 removed outlier: 3.731A pdb=" N SER C 6 " --> pdb=" O CYS C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.536A pdb=" N GLU C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.764A pdb=" N ILE C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.752A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.564A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.794A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.940A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 14 through 46 removed outlier: 4.126A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Proline residue: D 30 - end of helix Processing helix chain 'D' and resid 48 through 73 removed outlier: 3.828A pdb=" N VAL D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Proline residue: D 69 - end of helix Processing helix chain 'D' and resid 86 through 119 removed outlier: 4.133A pdb=" N LEU D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 128 through 154 removed outlier: 3.686A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 151 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 192 removed outlier: 3.540A pdb=" N ILE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Proline residue: D 183 - end of helix Processing helix chain 'D' and resid 193 through 213 removed outlier: 4.298A pdb=" N ARG D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 207 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL D 208 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 213 " --> pdb=" O TRP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 252 removed outlier: 3.514A pdb=" N ARG D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.594A pdb=" N TYR D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 278 removed outlier: 3.781A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.609A pdb=" N GLN E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.084A pdb=" N LEU A 90 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 103 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 92 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 removed outlier: 3.851A pdb=" N GLY A 126 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A 127 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN A 136 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 146 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.151A pdb=" N CYS A 160 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 169 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 181 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 187 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.555A pdb=" N PHE A 210 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 223 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.426A pdb=" N GLY A 255 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 243 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 253 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 256 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS A 261 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR A 274 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 263 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 289 removed outlier: 5.099A pdb=" N SER A 286 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 299 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS A 305 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL A 318 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 307 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 45 Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.575A pdb=" N ALA B 87 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG B 76 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TRP B 85 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.514A pdb=" N LEU B 212 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 228 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 214 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.357A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1164 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: 2.41 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2840 1.35 - 1.47: 2243 1.47 - 1.59: 3825 1.59 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 8990 Sorted by residual: bond pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN B 269 " pdb=" CG GLN B 269 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C TYR B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.08e+00 bond pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 1.803 1.828 -0.025 2.50e-02 1.60e+03 9.75e-01 bond pdb=" CA TRP D 81 " pdb=" CB TRP D 81 " ideal model delta sigma weight residual 1.530 1.516 0.013 1.38e-02 5.25e+03 9.33e-01 ... (remaining 8985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 12059 2.34 - 4.69: 93 4.69 - 7.03: 17 7.03 - 9.37: 5 9.37 - 11.72: 6 Bond angle restraints: 12180 Sorted by residual: angle pdb=" C ALA A 71 " pdb=" N MET A 72 " pdb=" CA MET A 72 " ideal model delta sigma weight residual 122.08 132.69 -10.61 1.84e+00 2.95e-01 3.33e+01 angle pdb=" CA MET A 72 " pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 114.10 124.74 -10.64 2.00e+00 2.50e-01 2.83e+01 angle pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta sigma weight residual 121.80 132.93 -11.13 2.44e+00 1.68e-01 2.08e+01 angle pdb=" CB MET A 72 " pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB MET D 79 " pdb=" CG MET D 79 " pdb=" SD MET D 79 " ideal model delta sigma weight residual 112.70 122.13 -9.43 3.00e+00 1.11e-01 9.88e+00 ... (remaining 12175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4438 17.78 - 35.56: 649 35.56 - 53.34: 195 53.34 - 71.13: 27 71.13 - 88.91: 5 Dihedral angle restraints: 5314 sinusoidal: 2064 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ARG A 161 " pdb=" C ARG A 161 " pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 246 " pdb=" C PHE A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 272 " pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1035 0.042 - 0.083: 264 0.083 - 0.125: 76 0.125 - 0.166: 5 0.166 - 0.208: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA TYR B 273 " pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CB TYR B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 284 " pdb=" N ILE A 284 " pdb=" C ILE A 284 " pdb=" CB ILE A 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CG LEU D 181 " pdb=" CB LEU D 181 " pdb=" CD1 LEU D 181 " pdb=" CD2 LEU D 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1378 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 273 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO B 274 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 71 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ALA A 71 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA A 71 " 0.017 2.00e-02 2.50e+03 pdb=" N MET A 72 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 140 " 0.013 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" CG TRP D 140 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 140 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 140 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 140 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 140 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 140 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 140 " 0.002 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 255 2.69 - 3.24: 8335 3.24 - 3.80: 13973 3.80 - 4.35: 17941 4.35 - 4.90: 30022 Nonbonded interactions: 70526 Sorted by model distance: nonbonded pdb=" O ILE A 69 " pdb=" OG SER A 327 " model vdw 2.140 3.040 nonbonded pdb=" O LEU D 263 " pdb=" OG1 THR D 266 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR B 211 " pdb=" OG SER C 6 " model vdw 2.185 3.040 nonbonded pdb=" OG SER A 342 " pdb=" OD1 ASP A 344 " model vdw 2.193 3.040 nonbonded pdb=" O GLN A 86 " pdb=" OG SER A 109 " model vdw 2.220 3.040 ... (remaining 70521 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=0.01 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.850 Find NCS groups from input model: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 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 0.038 8990 Z= 0.146 Angle : 0.618 11.718 12180 Z= 0.310 Chirality : 0.040 0.208 1381 Planarity : 0.004 0.106 1540 Dihedral : 17.794 88.907 3213 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.70 % Favored : 94.76 % Rotamer: Outliers : 0.42 % Allowed : 36.11 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1107 helix: 1.33 (0.27), residues: 388 sheet: 0.68 (0.33), residues: 245 loop : -1.38 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 140 HIS 0.004 0.001 HIS D 245 PHE 0.016 0.001 PHE B 241 TYR 0.019 0.001 TYR D 276 ARG 0.005 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.6730 (mtt90) cc_final: 0.6339 (mtt90) REVERT: A 338 VAL cc_start: 0.8515 (t) cc_final: 0.8208 (p) REVERT: C 198 MET cc_start: 0.7561 (tpp) cc_final: 0.7224 (tpp) outliers start: 4 outliers final: 2 residues processed: 220 average time/residue: 0.2553 time to fit residues: 73.6654 Evaluate side-chains 221 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain D residue 274 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN D 14 HIS E 18 GLN E 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8990 Z= 0.375 Angle : 0.701 12.163 12180 Z= 0.359 Chirality : 0.047 0.298 1381 Planarity : 0.005 0.084 1540 Dihedral : 4.865 43.412 1225 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.23 % Favored : 93.32 % Rotamer: Outliers : 6.97 % Allowed : 29.97 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1107 helix: 1.03 (0.26), residues: 405 sheet: 0.23 (0.32), residues: 262 loop : -1.52 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.009 0.002 HIS D 245 PHE 0.016 0.002 PHE A 210 TYR 0.018 0.002 TYR A 70 ARG 0.009 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7012 (mtt90) cc_final: 0.6568 (mtt90) REVERT: A 288 SER cc_start: 0.8494 (p) cc_final: 0.8009 (m) REVERT: A 338 VAL cc_start: 0.8620 (t) cc_final: 0.8318 (p) REVERT: A 346 PHE cc_start: 0.7903 (m-80) cc_final: 0.7622 (m-80) REVERT: B 97 TYR cc_start: 0.8058 (m-80) cc_final: 0.7741 (m-80) REVERT: B 107 THR cc_start: 0.7817 (t) cc_final: 0.7593 (m) REVERT: B 251 THR cc_start: 0.8099 (t) cc_final: 0.7887 (p) REVERT: C 186 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6089 (mt-10) REVERT: C 240 MET cc_start: 0.3463 (ttp) cc_final: 0.3053 (ttp) REVERT: C 243 MET cc_start: 0.7480 (ttm) cc_final: 0.7239 (ttm) REVERT: D 29 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7873 (mt) REVERT: D 46 ARG cc_start: 0.6519 (OUTLIER) cc_final: 0.6190 (ptt90) REVERT: D 151 TYR cc_start: 0.3524 (p90) cc_final: 0.2920 (p90) REVERT: D 206 ARG cc_start: 0.7162 (mtt90) cc_final: 0.6947 (mtt90) REVERT: E 37 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7992 (mp) outliers start: 67 outliers final: 45 residues processed: 278 average time/residue: 0.2426 time to fit residues: 89.3126 Evaluate side-chains 268 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN B 180 GLN C 188 HIS D 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8990 Z= 0.268 Angle : 0.633 11.409 12180 Z= 0.321 Chirality : 0.043 0.221 1381 Planarity : 0.005 0.062 1540 Dihedral : 4.548 24.842 1221 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.15 % Favored : 94.49 % Rotamer: Outliers : 7.80 % Allowed : 29.97 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1107 helix: 1.03 (0.26), residues: 401 sheet: 0.12 (0.32), residues: 265 loop : -1.60 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.009 0.001 HIS D 14 PHE 0.024 0.002 PHE C 189 TYR 0.018 0.002 TYR B 273 ARG 0.007 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6627 (mmp) REVERT: A 98 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 107 ARG cc_start: 0.6939 (mtt90) cc_final: 0.6494 (mtt90) REVERT: A 122 TYR cc_start: 0.8252 (m-80) cc_final: 0.7632 (m-80) REVERT: A 239 ASP cc_start: 0.7698 (p0) cc_final: 0.7278 (p0) REVERT: A 288 SER cc_start: 0.8505 (p) cc_final: 0.8271 (p) REVERT: A 301 ASP cc_start: 0.7061 (m-30) cc_final: 0.6715 (m-30) REVERT: A 338 VAL cc_start: 0.8652 (t) cc_final: 0.8318 (p) REVERT: B 107 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7657 (m) REVERT: B 250 PHE cc_start: 0.8342 (m-80) cc_final: 0.7626 (m-80) REVERT: B 251 THR cc_start: 0.8122 (t) cc_final: 0.7921 (p) REVERT: C 35 LYS cc_start: 0.8216 (mttp) cc_final: 0.7956 (mtmm) REVERT: C 36 LEU cc_start: 0.8565 (mt) cc_final: 0.8335 (mp) REVERT: C 209 LYS cc_start: 0.8306 (ptpp) cc_final: 0.8098 (ptpp) REVERT: C 231 ASP cc_start: 0.7516 (t0) cc_final: 0.7286 (t0) REVERT: C 240 MET cc_start: 0.3431 (ttp) cc_final: 0.3027 (ttp) REVERT: C 243 MET cc_start: 0.7340 (ttm) cc_final: 0.7093 (ttm) REVERT: C 261 ASP cc_start: 0.7345 (t0) cc_final: 0.7032 (t0) REVERT: D 29 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7773 (mt) REVERT: D 46 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.6128 (ptt90) REVERT: D 109 VAL cc_start: 0.8115 (m) cc_final: 0.7760 (p) REVERT: D 112 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: D 151 TYR cc_start: 0.3712 (p90) cc_final: 0.3024 (p90) REVERT: D 222 ARG cc_start: 0.7958 (tpt-90) cc_final: 0.7738 (tpt-90) outliers start: 75 outliers final: 44 residues processed: 272 average time/residue: 0.2510 time to fit residues: 90.2259 Evaluate side-chains 279 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 270 GLN C 331 ASN D 14 HIS D 146 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 8990 Z= 0.371 Angle : 0.690 14.131 12180 Z= 0.353 Chirality : 0.046 0.219 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.934 27.250 1221 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.14 % Favored : 93.50 % Rotamer: Outliers : 8.84 % Allowed : 28.93 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1107 helix: 0.84 (0.26), residues: 402 sheet: -0.20 (0.32), residues: 263 loop : -1.77 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 180 HIS 0.009 0.002 HIS D 14 PHE 0.026 0.002 PHE D 234 TYR 0.018 0.002 TYR D 202 ARG 0.005 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 233 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7677 (p0) REVERT: A 98 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7820 (p) REVERT: A 107 ARG cc_start: 0.6948 (mtt90) cc_final: 0.6556 (mtt90) REVERT: A 239 ASP cc_start: 0.7636 (p0) cc_final: 0.7179 (p0) REVERT: A 301 ASP cc_start: 0.7151 (m-30) cc_final: 0.6890 (m-30) REVERT: A 338 VAL cc_start: 0.8659 (t) cc_final: 0.8360 (p) REVERT: B 97 TYR cc_start: 0.8078 (m-80) cc_final: 0.7661 (m-80) REVERT: B 107 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7721 (m) REVERT: B 135 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.7966 (t) REVERT: B 250 PHE cc_start: 0.8224 (m-80) cc_final: 0.7598 (m-80) REVERT: C 35 LYS cc_start: 0.8199 (mttp) cc_final: 0.7909 (mtmm) REVERT: C 36 LEU cc_start: 0.8587 (mt) cc_final: 0.8355 (mp) REVERT: C 197 LYS cc_start: 0.7787 (mttm) cc_final: 0.7538 (mmtt) REVERT: C 209 LYS cc_start: 0.8347 (ptpp) cc_final: 0.8098 (ptpp) REVERT: C 231 ASP cc_start: 0.7647 (t0) cc_final: 0.7435 (t0) REVERT: C 240 MET cc_start: 0.3497 (ttp) cc_final: 0.3205 (ttp) REVERT: C 245 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7075 (tm-30) REVERT: C 247 MET cc_start: 0.7686 (mmm) cc_final: 0.7397 (mtt) REVERT: C 248 LYS cc_start: 0.7779 (ptpp) cc_final: 0.7574 (ptpp) REVERT: C 261 ASP cc_start: 0.7473 (t0) cc_final: 0.7147 (t0) REVERT: C 309 ASP cc_start: 0.7419 (m-30) cc_final: 0.7062 (m-30) REVERT: D 29 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7801 (mt) REVERT: D 46 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6155 (ptt90) REVERT: D 109 VAL cc_start: 0.8108 (m) cc_final: 0.7767 (p) REVERT: D 112 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: D 151 TYR cc_start: 0.3903 (OUTLIER) cc_final: 0.2999 (p90) REVERT: D 207 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7435 (tp) REVERT: D 222 ARG cc_start: 0.7943 (tpt-90) cc_final: 0.7720 (tpt-90) outliers start: 85 outliers final: 53 residues processed: 281 average time/residue: 0.2637 time to fit residues: 96.6096 Evaluate side-chains 291 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 250 ASN D 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8990 Z= 0.239 Angle : 0.642 13.834 12180 Z= 0.325 Chirality : 0.043 0.179 1381 Planarity : 0.005 0.065 1540 Dihedral : 4.670 25.746 1221 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 7.60 % Allowed : 30.39 % Favored : 62.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1107 helix: 0.97 (0.27), residues: 403 sheet: -0.21 (0.31), residues: 269 loop : -1.68 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 15 HIS 0.015 0.001 HIS D 14 PHE 0.028 0.002 PHE D 173 TYR 0.019 0.001 TYR D 202 ARG 0.004 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 216 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7228 (p0) REVERT: A 98 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7778 (p) REVERT: A 107 ARG cc_start: 0.6901 (mtt90) cc_final: 0.6487 (mtt90) REVERT: A 239 ASP cc_start: 0.7769 (p0) cc_final: 0.7334 (p0) REVERT: A 288 SER cc_start: 0.8466 (p) cc_final: 0.7795 (m) REVERT: A 301 ASP cc_start: 0.6998 (m-30) cc_final: 0.6711 (m-30) REVERT: A 338 VAL cc_start: 0.8686 (t) cc_final: 0.8403 (p) REVERT: B 97 TYR cc_start: 0.8092 (m-80) cc_final: 0.7649 (m-80) REVERT: B 107 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7719 (m) REVERT: B 227 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8415 (pt) REVERT: B 250 PHE cc_start: 0.8196 (m-80) cc_final: 0.7550 (m-80) REVERT: C 35 LYS cc_start: 0.8193 (mttp) cc_final: 0.7897 (mtpp) REVERT: C 36 LEU cc_start: 0.8621 (mt) cc_final: 0.8368 (mp) REVERT: C 186 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6283 (mt-10) REVERT: C 231 ASP cc_start: 0.7636 (t0) cc_final: 0.7425 (t0) REVERT: C 240 MET cc_start: 0.3412 (ttp) cc_final: 0.3173 (ttp) REVERT: C 245 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7026 (tm-30) REVERT: C 247 MET cc_start: 0.7672 (mmm) cc_final: 0.7362 (mtt) REVERT: C 261 ASP cc_start: 0.7405 (t0) cc_final: 0.6976 (t0) REVERT: C 309 ASP cc_start: 0.7399 (m-30) cc_final: 0.7043 (m-30) REVERT: D 15 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.6041 (p90) REVERT: D 29 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7733 (mt) REVERT: D 46 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6264 (ptt90) REVERT: D 109 VAL cc_start: 0.8100 (m) cc_final: 0.7750 (p) REVERT: D 112 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: D 126 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.6076 (mtm-85) REVERT: D 151 TYR cc_start: 0.3805 (OUTLIER) cc_final: 0.2916 (p90) REVERT: D 190 VAL cc_start: 0.6940 (OUTLIER) cc_final: 0.6727 (p) outliers start: 73 outliers final: 55 residues processed: 258 average time/residue: 0.2400 time to fit residues: 81.9741 Evaluate side-chains 275 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 210 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0870 chunk 26 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 61 optimal weight: 0.0980 overall best weight: 0.1072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN A 306 ASN D 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8990 Z= 0.151 Angle : 0.594 11.301 12180 Z= 0.299 Chirality : 0.041 0.186 1381 Planarity : 0.004 0.066 1540 Dihedral : 4.341 25.024 1221 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.15 % Favored : 94.49 % Rotamer: Outliers : 7.49 % Allowed : 30.49 % Favored : 62.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1107 helix: 1.28 (0.27), residues: 397 sheet: 0.06 (0.32), residues: 255 loop : -1.68 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 74 HIS 0.014 0.001 HIS D 14 PHE 0.027 0.001 PHE D 234 TYR 0.017 0.001 TYR D 202 ARG 0.009 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.6623 (p0) REVERT: A 98 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7800 (p) REVERT: A 107 ARG cc_start: 0.6866 (mtt90) cc_final: 0.6425 (mtt90) REVERT: A 226 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: A 239 ASP cc_start: 0.7756 (p0) cc_final: 0.7419 (p0) REVERT: A 288 SER cc_start: 0.8506 (p) cc_final: 0.7853 (m) REVERT: A 301 ASP cc_start: 0.6937 (m-30) cc_final: 0.6720 (m-30) REVERT: A 338 VAL cc_start: 0.8658 (t) cc_final: 0.8372 (p) REVERT: B 67 PHE cc_start: 0.8286 (t80) cc_final: 0.7958 (t80) REVERT: B 227 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8380 (pt) REVERT: C 186 GLU cc_start: 0.6464 (mt-10) cc_final: 0.6262 (mt-10) REVERT: C 231 ASP cc_start: 0.7627 (t0) cc_final: 0.7408 (t0) REVERT: C 240 MET cc_start: 0.3406 (ttp) cc_final: 0.3164 (ttp) REVERT: C 247 MET cc_start: 0.7628 (mmm) cc_final: 0.7266 (mtt) REVERT: C 261 ASP cc_start: 0.7231 (t0) cc_final: 0.6818 (t0) REVERT: C 309 ASP cc_start: 0.7369 (m-30) cc_final: 0.7001 (m-30) REVERT: D 15 TRP cc_start: 0.6693 (OUTLIER) cc_final: 0.5732 (p90) REVERT: D 29 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7655 (mt) REVERT: D 46 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6277 (ptt90) REVERT: D 112 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: D 113 ARG cc_start: 0.8346 (mtt180) cc_final: 0.8012 (mtt180) REVERT: D 126 ARG cc_start: 0.6689 (mtm-85) cc_final: 0.6065 (mtm-85) REVERT: D 151 TYR cc_start: 0.3881 (OUTLIER) cc_final: 0.3041 (p90) outliers start: 72 outliers final: 45 residues processed: 263 average time/residue: 0.2475 time to fit residues: 86.0256 Evaluate side-chains 277 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN D 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8990 Z= 0.263 Angle : 0.641 12.418 12180 Z= 0.324 Chirality : 0.044 0.212 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.570 24.464 1221 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.78 % Favored : 93.86 % Rotamer: Outliers : 6.76 % Allowed : 31.01 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1107 helix: 1.10 (0.27), residues: 402 sheet: -0.13 (0.32), residues: 263 loop : -1.73 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 180 HIS 0.010 0.001 HIS D 14 PHE 0.029 0.002 PHE D 234 TYR 0.018 0.002 TYR D 202 ARG 0.013 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 217 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7815 (p) REVERT: A 107 ARG cc_start: 0.6903 (mtt90) cc_final: 0.6451 (mtt90) REVERT: A 226 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.6124 (mp0) REVERT: A 239 ASP cc_start: 0.7773 (p0) cc_final: 0.7368 (p0) REVERT: A 288 SER cc_start: 0.8483 (p) cc_final: 0.7827 (m) REVERT: A 301 ASP cc_start: 0.6980 (m-30) cc_final: 0.6673 (m-30) REVERT: A 338 VAL cc_start: 0.8676 (t) cc_final: 0.8398 (p) REVERT: B 227 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8423 (pt) REVERT: C 33 GLU cc_start: 0.7226 (tt0) cc_final: 0.6909 (tt0) REVERT: C 36 LEU cc_start: 0.8617 (mt) cc_final: 0.8205 (mt) REVERT: C 197 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7320 (mttm) REVERT: C 240 MET cc_start: 0.3448 (ttp) cc_final: 0.3235 (ttp) REVERT: C 247 MET cc_start: 0.7643 (mmm) cc_final: 0.7308 (mtt) REVERT: C 261 ASP cc_start: 0.7417 (t0) cc_final: 0.6983 (t0) REVERT: C 309 ASP cc_start: 0.7418 (m-30) cc_final: 0.7043 (m-30) REVERT: D 15 TRP cc_start: 0.6867 (OUTLIER) cc_final: 0.6147 (p90) REVERT: D 29 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7689 (mt) REVERT: D 46 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6289 (ptt90) REVERT: D 112 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: D 126 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6095 (mtm-85) REVERT: D 151 TYR cc_start: 0.3907 (OUTLIER) cc_final: 0.3019 (p90) outliers start: 65 outliers final: 49 residues processed: 256 average time/residue: 0.2364 time to fit residues: 80.5083 Evaluate side-chains 272 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 93 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8990 Z= 0.249 Angle : 0.636 12.720 12180 Z= 0.321 Chirality : 0.043 0.204 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.567 24.371 1221 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.51 % Favored : 94.13 % Rotamer: Outliers : 7.18 % Allowed : 31.11 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1107 helix: 1.09 (0.27), residues: 402 sheet: -0.18 (0.32), residues: 262 loop : -1.73 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 180 HIS 0.016 0.001 HIS D 14 PHE 0.018 0.002 PHE D 234 TYR 0.021 0.001 TYR D 202 ARG 0.013 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7816 (p) REVERT: A 107 ARG cc_start: 0.6893 (mtt90) cc_final: 0.6446 (mtt90) REVERT: A 226 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: A 239 ASP cc_start: 0.7797 (p0) cc_final: 0.7411 (p0) REVERT: A 288 SER cc_start: 0.8482 (p) cc_final: 0.8230 (p) REVERT: A 301 ASP cc_start: 0.6938 (m-30) cc_final: 0.6626 (m-30) REVERT: A 338 VAL cc_start: 0.8684 (t) cc_final: 0.8382 (p) REVERT: C 36 LEU cc_start: 0.8618 (mt) cc_final: 0.8209 (mt) REVERT: C 197 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7357 (mttm) REVERT: C 245 GLU cc_start: 0.7486 (tm-30) cc_final: 0.7031 (tm-30) REVERT: C 247 MET cc_start: 0.7639 (mmm) cc_final: 0.7345 (mtt) REVERT: C 261 ASP cc_start: 0.7426 (t0) cc_final: 0.7002 (t0) REVERT: C 309 ASP cc_start: 0.7423 (m-30) cc_final: 0.7038 (m-30) REVERT: D 15 TRP cc_start: 0.6879 (OUTLIER) cc_final: 0.6102 (p90) REVERT: D 29 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7695 (mt) REVERT: D 46 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6286 (ptt90) REVERT: D 112 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: D 126 ARG cc_start: 0.6706 (mtm-85) cc_final: 0.6035 (mtm-85) REVERT: D 151 TYR cc_start: 0.3876 (OUTLIER) cc_final: 0.3007 (p90) outliers start: 69 outliers final: 54 residues processed: 256 average time/residue: 0.2330 time to fit residues: 79.7299 Evaluate side-chains 274 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.0170 chunk 65 optimal weight: 0.0470 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8990 Z= 0.218 Angle : 0.636 12.866 12180 Z= 0.322 Chirality : 0.043 0.212 1381 Planarity : 0.005 0.065 1540 Dihedral : 4.525 25.342 1221 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.24 % Favored : 94.40 % Rotamer: Outliers : 7.49 % Allowed : 31.32 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1107 helix: 1.13 (0.27), residues: 402 sheet: -0.32 (0.31), residues: 268 loop : -1.69 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.021 0.001 HIS D 14 PHE 0.020 0.002 PHE D 234 TYR 0.020 0.001 TYR D 202 ARG 0.014 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7217 (ptp-110) cc_final: 0.6827 (ptp-110) REVERT: A 98 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7798 (p) REVERT: A 107 ARG cc_start: 0.6872 (mtt90) cc_final: 0.6437 (mtt90) REVERT: A 122 TYR cc_start: 0.8359 (m-80) cc_final: 0.7630 (m-80) REVERT: A 226 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: A 239 ASP cc_start: 0.7802 (p0) cc_final: 0.7414 (p0) REVERT: A 288 SER cc_start: 0.8478 (p) cc_final: 0.8223 (p) REVERT: A 301 ASP cc_start: 0.6928 (m-30) cc_final: 0.6623 (m-30) REVERT: A 315 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7077 (ttm170) REVERT: A 338 VAL cc_start: 0.8679 (t) cc_final: 0.8377 (p) REVERT: B 67 PHE cc_start: 0.8233 (t80) cc_final: 0.7857 (t80) REVERT: C 197 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7589 (mttm) REVERT: C 198 MET cc_start: 0.8087 (mtp) cc_final: 0.7848 (ttm) REVERT: C 245 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7027 (tm-30) REVERT: C 247 MET cc_start: 0.7640 (mmm) cc_final: 0.7343 (mtt) REVERT: C 261 ASP cc_start: 0.7411 (t0) cc_final: 0.6986 (t0) REVERT: C 309 ASP cc_start: 0.7414 (m-30) cc_final: 0.7022 (m-30) REVERT: D 15 TRP cc_start: 0.6820 (OUTLIER) cc_final: 0.5773 (p90) REVERT: D 29 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7684 (mt) REVERT: D 46 ARG cc_start: 0.6532 (OUTLIER) cc_final: 0.6298 (ptt90) REVERT: D 112 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: D 126 ARG cc_start: 0.6711 (mtm-85) cc_final: 0.6080 (mtm-85) REVERT: D 151 TYR cc_start: 0.4062 (OUTLIER) cc_final: 0.3176 (p90) outliers start: 72 outliers final: 57 residues processed: 257 average time/residue: 0.2368 time to fit residues: 81.3927 Evaluate side-chains 279 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 215 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8990 Z= 0.215 Angle : 0.637 13.334 12180 Z= 0.322 Chirality : 0.043 0.221 1381 Planarity : 0.005 0.065 1540 Dihedral : 4.490 25.623 1221 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.33 % Favored : 94.31 % Rotamer: Outliers : 7.18 % Allowed : 31.53 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.26), residues: 1107 helix: 1.16 (0.27), residues: 402 sheet: -0.20 (0.32), residues: 262 loop : -1.71 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.016 0.001 HIS D 14 PHE 0.030 0.002 PHE D 234 TYR 0.019 0.001 TYR D 202 ARG 0.008 0.000 ARG A 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 206 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.7184 (ptp-110) cc_final: 0.6784 (ptp-110) REVERT: A 98 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 107 ARG cc_start: 0.6865 (mtt90) cc_final: 0.6422 (mtt90) REVERT: A 122 TYR cc_start: 0.8355 (m-80) cc_final: 0.7635 (m-80) REVERT: A 226 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: A 239 ASP cc_start: 0.7808 (p0) cc_final: 0.7436 (p0) REVERT: A 288 SER cc_start: 0.8471 (p) cc_final: 0.8215 (p) REVERT: A 301 ASP cc_start: 0.6912 (m-30) cc_final: 0.6623 (m-30) REVERT: A 338 VAL cc_start: 0.8679 (t) cc_final: 0.8374 (p) REVERT: B 67 PHE cc_start: 0.8240 (t80) cc_final: 0.7855 (t80) REVERT: C 197 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7635 (mmtm) REVERT: C 198 MET cc_start: 0.8065 (mtp) cc_final: 0.7826 (ttm) REVERT: C 245 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6995 (tm-30) REVERT: C 261 ASP cc_start: 0.7408 (t0) cc_final: 0.6966 (t0) REVERT: C 309 ASP cc_start: 0.7463 (m-30) cc_final: 0.7097 (m-30) REVERT: D 15 TRP cc_start: 0.6800 (OUTLIER) cc_final: 0.5675 (p90) REVERT: D 29 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7650 (mt) REVERT: D 46 ARG cc_start: 0.6539 (OUTLIER) cc_final: 0.6269 (ptt90) REVERT: D 112 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: D 126 ARG cc_start: 0.6696 (mtm-85) cc_final: 0.6072 (mtm-85) REVERT: D 151 TYR cc_start: 0.4046 (OUTLIER) cc_final: 0.3160 (p90) outliers start: 69 outliers final: 58 residues processed: 248 average time/residue: 0.2370 time to fit residues: 78.4637 Evaluate side-chains 272 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 146 HIS Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.146987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127750 restraints weight = 13353.398| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.12 r_work: 0.3419 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8990 Z= 0.287 Angle : 0.668 14.079 12180 Z= 0.339 Chirality : 0.045 0.230 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.640 25.272 1221 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 7.28 % Allowed : 31.53 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1107 helix: 1.06 (0.27), residues: 402 sheet: -0.25 (0.32), residues: 262 loop : -1.76 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 180 HIS 0.016 0.002 HIS D 14 PHE 0.022 0.002 PHE D 234 TYR 0.018 0.002 TYR D 202 ARG 0.008 0.000 ARG A 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.47 seconds wall clock time: 48 minutes 1.17 seconds (2881.17 seconds total)