Starting phenix.real_space_refine on Tue Mar 3 22:55:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6u_25728/03_2026/7t6u_25728.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6u_25728/03_2026/7t6u_25728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t6u_25728/03_2026/7t6u_25728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6u_25728/03_2026/7t6u_25728.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t6u_25728/03_2026/7t6u_25728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6u_25728/03_2026/7t6u_25728.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5791 2.51 5 N 1516 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9033 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1763 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1784 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "R" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2346 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 285} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.83, per 1000 atoms: 0.20 Number of scatterers: 9033 At special positions: 0 Unit cell: (118.8, 115.56, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1662 8.00 N 1516 7.00 C 5791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 319.0 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QXV L 21 " Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 38.9% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.948A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.514A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.595A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.163A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.721A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.687A pdb=" N LEU A 273 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 275 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.153A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.748A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.556A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.758A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.616A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.002A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 39 Proline residue: R 29 - end of helix Processing helix chain 'R' and resid 39 through 54 removed outlier: 3.757A pdb=" N VAL R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY R 52 " --> pdb=" O ILE R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 76 removed outlier: 4.121A pdb=" N PHE R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 87 removed outlier: 3.613A pdb=" N VAL R 83 " --> pdb=" O PRO R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 129 removed outlier: 3.652A pdb=" N HIS R 102 " --> pdb=" O CYS R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 137 removed outlier: 3.610A pdb=" N ALA R 133 " --> pdb=" O HIS R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 removed outlier: 3.815A pdb=" N LYS R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 157 Processing helix chain 'R' and resid 157 through 163 Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 189 through 207 removed outlier: 3.824A pdb=" N VAL R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 231 removed outlier: 3.737A pdb=" N ILE R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA R 225 " --> pdb=" O TYR R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 253 removed outlier: 3.568A pdb=" N VAL R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 267 removed outlier: 3.730A pdb=" N VAL R 260 " --> pdb=" O PRO R 256 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 275 Processing helix chain 'R' and resid 277 through 293 removed outlier: 4.066A pdb=" N ASP R 281 " --> pdb=" O TYR R 277 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix removed outlier: 3.594A pdb=" N LEU R 290 " --> pdb=" O PRO R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 removed outlier: 3.566A pdb=" N LEU R 297 " --> pdb=" O PHE R 293 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 315 removed outlier: 3.545A pdb=" N HIS R 315 " --> pdb=" O GLU R 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.169A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.508A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.828A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.541A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.832A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.539A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.017A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.011A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.011A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.731A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'R' and resid 164 through 168 removed outlier: 3.709A pdb=" N THR R 177 " --> pdb=" O THR R 165 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1449 1.31 - 1.43: 2518 1.43 - 1.56: 5163 1.56 - 1.69: 1 1.69 - 1.81: 94 Bond restraints: 9225 Sorted by residual: bond pdb=" C QXV L 21 " pdb=" NXT QXV L 21 " ideal model delta sigma weight residual 1.339 1.445 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.61e-02 3.86e+03 1.48e+01 bond pdb=" N TYR R 274 " pdb=" CA TYR R 274 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.06e-02 8.90e+03 1.19e+01 bond pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N VAL R 284 " pdb=" CA VAL R 284 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 11735 1.91 - 3.82: 619 3.82 - 5.73: 97 5.73 - 7.64: 29 7.64 - 9.55: 6 Bond angle restraints: 12486 Sorted by residual: angle pdb=" N PHE R 163 " pdb=" CA PHE R 163 " pdb=" C PHE R 163 " ideal model delta sigma weight residual 112.94 119.73 -6.79 1.41e+00 5.03e-01 2.32e+01 angle pdb=" N LEU R 263 " pdb=" CA LEU R 263 " pdb=" C LEU R 263 " ideal model delta sigma weight residual 111.82 106.40 5.42 1.16e+00 7.43e-01 2.18e+01 angle pdb=" C ASN R 285 " pdb=" CA ASN R 285 " pdb=" CB ASN R 285 " ideal model delta sigma weight residual 113.04 120.59 -7.55 1.63e+00 3.76e-01 2.15e+01 angle pdb=" N PRO R 286 " pdb=" CA PRO R 286 " pdb=" CB PRO R 286 " ideal model delta sigma weight residual 103.33 98.30 5.03 1.10e+00 8.26e-01 2.09e+01 angle pdb=" CA CYS R 176 " pdb=" C CYS R 176 " pdb=" O CYS R 176 " ideal model delta sigma weight residual 121.58 116.47 5.11 1.12e+00 7.97e-01 2.08e+01 ... (remaining 12481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 4947 16.90 - 33.80: 411 33.80 - 50.70: 76 50.70 - 67.60: 11 67.60 - 84.50: 5 Dihedral angle restraints: 5450 sinusoidal: 2131 harmonic: 3319 Sorted by residual: dihedral pdb=" CB CYS R 98 " pdb=" SG CYS R 98 " pdb=" SG CYS R 176 " pdb=" CB CYS R 176 " ideal model delta sinusoidal sigma weight residual -86.00 -170.50 84.50 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CA GLU A 276 " pdb=" C GLU A 276 " pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" C ASN R 285 " pdb=" N ASN R 285 " pdb=" CA ASN R 285 " pdb=" CB ASN R 285 " ideal model delta harmonic sigma weight residual -122.60 -137.44 14.84 0 2.50e+00 1.60e-01 3.52e+01 ... (remaining 5447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1278 0.098 - 0.196: 127 0.196 - 0.293: 11 0.293 - 0.391: 4 0.391 - 0.489: 2 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA ASN R 285 " pdb=" N ASN R 285 " pdb=" C ASN R 285 " pdb=" CB ASN R 285 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA GLU R 270 " pdb=" N GLU R 270 " pdb=" C GLU R 270 " pdb=" CB GLU R 270 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CA ASN R 135 " pdb=" N ASN R 135 " pdb=" C ASN R 135 " pdb=" CB ASN R 135 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1419 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO R 149 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 238 " 0.046 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO R 239 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 255 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO R 256 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 256 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 256 " -0.038 5.00e-02 4.00e+02 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2867 2.83 - 3.35: 7718 3.35 - 3.87: 15014 3.87 - 4.38: 17756 4.38 - 4.90: 30643 Nonbonded interactions: 73998 Sorted by model distance: nonbonded pdb=" OD2 ASP A 231 " pdb=" OG SER A 281 " model vdw 2.315 3.040 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.334 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.335 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.346 3.040 nonbonded pdb=" OE2 GLU A 28 " pdb=" OG SER R 140 " model vdw 2.347 3.040 ... (remaining 73993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.006 0.106 9228 Z= 0.323 Angle : 1.001 9.546 12492 Z= 0.635 Chirality : 0.064 0.489 1422 Planarity : 0.007 0.069 1565 Dihedral : 12.927 81.902 3301 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.31 % Allowed : 5.40 % Favored : 94.29 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.20), residues: 1133 helix: -4.08 (0.14), residues: 399 sheet: -0.94 (0.28), residues: 284 loop : -1.88 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 242 TYR 0.025 0.002 TYR R 175 PHE 0.018 0.002 PHE R 163 TRP 0.014 0.002 TRP R 132 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00574 ( 9225) covalent geometry : angle 0.99990 (12486) SS BOND : bond 0.00367 ( 3) SS BOND : angle 1.88065 ( 6) hydrogen bonds : bond 0.27804 ( 427) hydrogen bonds : angle 10.34121 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7859 (mtmm) REVERT: A 20 ASP cc_start: 0.7182 (p0) cc_final: 0.6953 (p0) REVERT: A 29 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7776 (mtpm) REVERT: A 186 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7005 (mt-10) REVERT: A 197 LYS cc_start: 0.7706 (mttt) cc_final: 0.7337 (mttm) REVERT: A 207 GLU cc_start: 0.7364 (tt0) cc_final: 0.7161 (tt0) REVERT: A 209 LYS cc_start: 0.7576 (ttpp) cc_final: 0.7252 (ttpp) REVERT: A 243 MET cc_start: 0.7534 (ttm) cc_final: 0.7160 (ttm) REVERT: A 245 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6981 (mm-30) REVERT: A 248 LYS cc_start: 0.7620 (ttmm) cc_final: 0.7347 (ttmm) REVERT: A 252 SER cc_start: 0.8215 (m) cc_final: 0.7938 (m) REVERT: A 271 LYS cc_start: 0.8393 (pttt) cc_final: 0.8105 (pttp) REVERT: A 294 ASN cc_start: 0.7803 (t0) cc_final: 0.7538 (t0) REVERT: A 309 ASP cc_start: 0.7273 (m-30) cc_final: 0.6922 (m-30) REVERT: A 318 GLU cc_start: 0.6838 (tp30) cc_final: 0.6612 (tp30) REVERT: B 147 SER cc_start: 0.8321 (m) cc_final: 0.8062 (p) REVERT: B 161 SER cc_start: 0.7917 (t) cc_final: 0.7698 (p) REVERT: B 163 ASP cc_start: 0.7317 (p0) cc_final: 0.6557 (p0) REVERT: B 186 ASP cc_start: 0.7521 (m-30) cc_final: 0.7281 (m-30) REVERT: B 217 MET cc_start: 0.6746 (mmm) cc_final: 0.6475 (mmm) REVERT: B 258 ASP cc_start: 0.7305 (t0) cc_final: 0.6696 (t0) REVERT: E 43 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8367 (ttmm) REVERT: E 84 THR cc_start: 0.8302 (m) cc_final: 0.7830 (p) REVERT: E 85 SER cc_start: 0.8373 (m) cc_final: 0.8019 (p) REVERT: E 155 VAL cc_start: 0.8654 (p) cc_final: 0.8301 (m) REVERT: E 186 GLN cc_start: 0.8114 (pt0) cc_final: 0.7801 (pt0) REVERT: E 210 THR cc_start: 0.7679 (p) cc_final: 0.7389 (m) REVERT: E 219 LEU cc_start: 0.8320 (tt) cc_final: 0.8118 (tm) REVERT: R 69 LEU cc_start: 0.8274 (mp) cc_final: 0.7859 (mp) REVERT: R 83 VAL cc_start: 0.7717 (p) cc_final: 0.7494 (m) REVERT: R 103 ILE cc_start: 0.8112 (mt) cc_final: 0.7902 (mm) REVERT: R 136 HIS cc_start: 0.7941 (m90) cc_final: 0.7728 (m-70) REVERT: R 214 MET cc_start: 0.7861 (tpp) cc_final: 0.7433 (tpp) REVERT: R 304 PHE cc_start: 0.7928 (m-10) cc_final: 0.7716 (m-80) outliers start: 3 outliers final: 1 residues processed: 251 average time/residue: 0.5677 time to fit residues: 151.8186 Evaluate side-chains 205 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 166 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 311 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 62 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 230 ASN B 237 ASN B 239 ASN B 259 GLN B 293 ASN E 194 ASN R 102 HIS R 108 ASN R 258 GLN R 307 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101696 restraints weight = 12498.730| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.73 r_work: 0.3207 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9228 Z= 0.138 Angle : 0.576 10.687 12492 Z= 0.307 Chirality : 0.043 0.139 1422 Planarity : 0.005 0.052 1565 Dihedral : 5.266 72.267 1266 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.06 % Allowed : 13.25 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.22), residues: 1133 helix: -1.40 (0.22), residues: 402 sheet: -0.55 (0.28), residues: 293 loop : -1.30 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 310 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE B 235 TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9225) covalent geometry : angle 0.57610 (12486) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.76693 ( 6) hydrogen bonds : bond 0.04440 ( 427) hydrogen bonds : angle 5.48416 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8212 (mtm) REVERT: A 51 LYS cc_start: 0.8468 (mttm) cc_final: 0.8137 (mttm) REVERT: A 186 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 197 LYS cc_start: 0.8361 (mttt) cc_final: 0.8036 (mttp) REVERT: A 209 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7878 (ttpp) REVERT: A 245 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 271 LYS cc_start: 0.8740 (pttt) cc_final: 0.8403 (pttp) REVERT: A 283 LEU cc_start: 0.8637 (tp) cc_final: 0.8279 (tm) REVERT: A 294 ASN cc_start: 0.7872 (t0) cc_final: 0.7665 (t0) REVERT: A 309 ASP cc_start: 0.7782 (m-30) cc_final: 0.7450 (m-30) REVERT: A 318 GLU cc_start: 0.7510 (tp30) cc_final: 0.7307 (tp30) REVERT: B 38 ASP cc_start: 0.8390 (m-30) cc_final: 0.8074 (m-30) REVERT: B 65 THR cc_start: 0.7925 (p) cc_final: 0.7719 (m) REVERT: B 147 SER cc_start: 0.8567 (m) cc_final: 0.8247 (p) REVERT: B 150 ARG cc_start: 0.8788 (mmt-90) cc_final: 0.8505 (mpt180) REVERT: B 163 ASP cc_start: 0.7626 (p0) cc_final: 0.7134 (p0) REVERT: B 217 MET cc_start: 0.7761 (mmm) cc_final: 0.7475 (mmm) REVERT: B 293 ASN cc_start: 0.8044 (m-40) cc_final: 0.7622 (m110) REVERT: B 312 ASP cc_start: 0.7904 (m-30) cc_final: 0.7556 (m-30) REVERT: B 338 ILE cc_start: 0.8643 (mm) cc_final: 0.8436 (mp) REVERT: E 25 SER cc_start: 0.8416 (t) cc_final: 0.8203 (p) REVERT: E 43 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8440 (ttmm) REVERT: E 67 ARG cc_start: 0.8532 (mtm110) cc_final: 0.8257 (mtm-85) REVERT: E 68 PHE cc_start: 0.8268 (m-10) cc_final: 0.7990 (m-10) REVERT: E 84 THR cc_start: 0.8501 (m) cc_final: 0.8069 (p) REVERT: E 85 SER cc_start: 0.8673 (m) cc_final: 0.8459 (p) REVERT: E 155 VAL cc_start: 0.8614 (p) cc_final: 0.8406 (t) REVERT: E 186 GLN cc_start: 0.8460 (pt0) cc_final: 0.8237 (pt0) REVERT: E 210 THR cc_start: 0.7885 (p) cc_final: 0.7567 (m) REVERT: R 42 LEU cc_start: 0.8192 (mp) cc_final: 0.7957 (mt) REVERT: R 54 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7642 (mtp85) REVERT: R 69 LEU cc_start: 0.8448 (mp) cc_final: 0.8130 (mp) REVERT: R 137 ARG cc_start: 0.8496 (ttt-90) cc_final: 0.7996 (ttt90) REVERT: R 211 SER cc_start: 0.8295 (t) cc_final: 0.8085 (p) REVERT: R 288 SER cc_start: 0.8302 (p) cc_final: 0.7999 (m) outliers start: 30 outliers final: 16 residues processed: 248 average time/residue: 0.6088 time to fit residues: 160.4593 Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.1980 chunk 82 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 237 ASN B 239 ASN R 66 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100284 restraints weight = 12452.475| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.72 r_work: 0.3195 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9228 Z= 0.147 Angle : 0.550 8.105 12492 Z= 0.288 Chirality : 0.043 0.138 1422 Planarity : 0.004 0.048 1565 Dihedral : 4.953 65.324 1265 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.98 % Allowed : 15.80 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1133 helix: -0.18 (0.25), residues: 409 sheet: -0.45 (0.28), residues: 295 loop : -1.06 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 310 TYR 0.013 0.001 TYR E 190 PHE 0.014 0.001 PHE B 235 TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9225) covalent geometry : angle 0.54997 (12486) SS BOND : bond 0.00339 ( 3) SS BOND : angle 0.65921 ( 6) hydrogen bonds : bond 0.03920 ( 427) hydrogen bonds : angle 5.03856 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: A 32 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7921 (ttm-80) REVERT: A 186 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 197 LYS cc_start: 0.8357 (mttt) cc_final: 0.8037 (mttp) REVERT: A 209 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7865 (ttpp) REVERT: A 245 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 271 LYS cc_start: 0.8779 (pttt) cc_final: 0.8455 (pttp) REVERT: A 283 LEU cc_start: 0.8639 (tp) cc_final: 0.8278 (tm) REVERT: A 309 ASP cc_start: 0.7726 (m-30) cc_final: 0.7322 (m-30) REVERT: A 318 GLU cc_start: 0.7551 (tp30) cc_final: 0.7329 (tp30) REVERT: B 38 ASP cc_start: 0.8385 (m-30) cc_final: 0.8100 (m-30) REVERT: B 45 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8353 (mtm) REVERT: B 132 ASN cc_start: 0.8235 (p0) cc_final: 0.8030 (p0) REVERT: B 134 ARG cc_start: 0.8445 (mtm110) cc_final: 0.8207 (ttp80) REVERT: B 147 SER cc_start: 0.8571 (m) cc_final: 0.8222 (p) REVERT: B 150 ARG cc_start: 0.8825 (mmt-90) cc_final: 0.8503 (mpt180) REVERT: B 163 ASP cc_start: 0.7466 (p0) cc_final: 0.7116 (p0) REVERT: B 217 MET cc_start: 0.7803 (mmm) cc_final: 0.7544 (mmm) REVERT: B 312 ASP cc_start: 0.7933 (m-30) cc_final: 0.7597 (m-30) REVERT: E 25 SER cc_start: 0.8475 (t) cc_final: 0.8270 (p) REVERT: E 43 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8406 (ttmm) REVERT: E 67 ARG cc_start: 0.8607 (mtm110) cc_final: 0.8386 (mtp180) REVERT: E 84 THR cc_start: 0.8504 (m) cc_final: 0.8059 (p) REVERT: E 85 SER cc_start: 0.8678 (m) cc_final: 0.8444 (p) REVERT: E 155 VAL cc_start: 0.8602 (p) cc_final: 0.8394 (t) REVERT: E 186 GLN cc_start: 0.8486 (pt0) cc_final: 0.8255 (pt0) REVERT: E 191 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.6730 (mtp180) REVERT: E 210 THR cc_start: 0.7886 (p) cc_final: 0.7595 (m) REVERT: R 54 ARG cc_start: 0.7838 (mmm160) cc_final: 0.7557 (mtp85) REVERT: R 58 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7825 (p) REVERT: R 69 LEU cc_start: 0.8457 (mp) cc_final: 0.8228 (mp) REVERT: R 137 ARG cc_start: 0.8572 (ttt-90) cc_final: 0.8290 (ttt180) REVERT: R 165 THR cc_start: 0.8430 (t) cc_final: 0.8073 (p) REVERT: R 201 ARG cc_start: 0.8129 (ttt90) cc_final: 0.7585 (ttt90) REVERT: R 266 VAL cc_start: 0.8224 (t) cc_final: 0.7874 (m) REVERT: R 283 LEU cc_start: 0.8067 (mt) cc_final: 0.7815 (mt) REVERT: R 284 VAL cc_start: 0.7942 (p) cc_final: 0.7668 (t) REVERT: R 288 SER cc_start: 0.8357 (p) cc_final: 0.8087 (m) REVERT: R 304 PHE cc_start: 0.8214 (m-10) cc_final: 0.7947 (m-80) outliers start: 39 outliers final: 18 residues processed: 236 average time/residue: 0.6203 time to fit residues: 155.1621 Evaluate side-chains 230 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 65 optimal weight: 0.0030 chunk 3 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 237 ASN B 293 ASN E 39 GLN E 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100893 restraints weight = 12674.636| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.75 r_work: 0.3204 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9228 Z= 0.119 Angle : 0.526 8.602 12492 Z= 0.274 Chirality : 0.042 0.141 1422 Planarity : 0.004 0.045 1565 Dihedral : 4.759 63.074 1265 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.98 % Allowed : 17.13 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1133 helix: 0.40 (0.26), residues: 415 sheet: -0.37 (0.29), residues: 282 loop : -0.91 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 201 TYR 0.014 0.001 TYR A 230 PHE 0.020 0.001 PHE R 163 TRP 0.016 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9225) covalent geometry : angle 0.52580 (12486) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.63072 ( 6) hydrogen bonds : bond 0.03479 ( 427) hydrogen bonds : angle 4.83801 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.346 Fit side-chains REVERT: A 18 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8227 (mtm) REVERT: A 32 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7953 (ttm-80) REVERT: A 186 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 197 LYS cc_start: 0.8360 (mttt) cc_final: 0.8040 (mttp) REVERT: A 209 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7813 (ttpp) REVERT: A 210 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8253 (mmtt) REVERT: A 245 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 271 LYS cc_start: 0.8788 (pttt) cc_final: 0.8478 (pttp) REVERT: A 283 LEU cc_start: 0.8648 (tp) cc_final: 0.8302 (tm) REVERT: A 309 ASP cc_start: 0.7756 (m-30) cc_final: 0.7367 (m-30) REVERT: A 318 GLU cc_start: 0.7520 (tp30) cc_final: 0.7298 (tp30) REVERT: A 337 ASP cc_start: 0.8049 (m-30) cc_final: 0.7777 (m-30) REVERT: B 38 ASP cc_start: 0.8365 (m-30) cc_final: 0.8090 (m-30) REVERT: B 132 ASN cc_start: 0.8239 (p0) cc_final: 0.8025 (p0) REVERT: B 147 SER cc_start: 0.8542 (m) cc_final: 0.8240 (p) REVERT: B 163 ASP cc_start: 0.7506 (p0) cc_final: 0.7122 (p0) REVERT: B 197 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.6608 (mtp85) REVERT: B 217 MET cc_start: 0.7803 (mmm) cc_final: 0.7572 (mmm) REVERT: B 312 ASP cc_start: 0.7971 (m-30) cc_final: 0.7624 (m-30) REVERT: E 25 SER cc_start: 0.8485 (t) cc_final: 0.8276 (p) REVERT: E 67 ARG cc_start: 0.8543 (mtm110) cc_final: 0.8301 (mtm-85) REVERT: E 84 THR cc_start: 0.8503 (m) cc_final: 0.8069 (p) REVERT: E 85 SER cc_start: 0.8706 (m) cc_final: 0.8483 (p) REVERT: E 186 GLN cc_start: 0.8483 (pt0) cc_final: 0.8178 (pt0) REVERT: E 191 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.6600 (mtp180) REVERT: E 210 THR cc_start: 0.7968 (p) cc_final: 0.7670 (m) REVERT: R 41 VAL cc_start: 0.8594 (t) cc_final: 0.8275 (p) REVERT: R 54 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7580 (mtp85) REVERT: R 56 THR cc_start: 0.8677 (t) cc_final: 0.8372 (p) REVERT: R 58 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7855 (p) REVERT: R 69 LEU cc_start: 0.8450 (mp) cc_final: 0.8179 (mp) REVERT: R 137 ARG cc_start: 0.8568 (ttt-90) cc_final: 0.8163 (ttt90) REVERT: R 165 THR cc_start: 0.8389 (t) cc_final: 0.8047 (p) REVERT: R 201 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7696 (ttt-90) REVERT: R 266 VAL cc_start: 0.8237 (t) cc_final: 0.7892 (m) REVERT: R 283 LEU cc_start: 0.8065 (mt) cc_final: 0.7800 (mt) REVERT: R 284 VAL cc_start: 0.7992 (p) cc_final: 0.7701 (t) REVERT: R 288 SER cc_start: 0.8369 (p) cc_final: 0.8124 (m) REVERT: R 304 PHE cc_start: 0.8211 (m-10) cc_final: 0.7999 (m-80) outliers start: 39 outliers final: 20 residues processed: 232 average time/residue: 0.6221 time to fit residues: 153.2261 Evaluate side-chains 240 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 103 optimal weight: 0.0470 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 155 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100635 restraints weight = 12601.521| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.72 r_work: 0.3203 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9228 Z= 0.134 Angle : 0.536 10.719 12492 Z= 0.276 Chirality : 0.043 0.137 1422 Planarity : 0.004 0.043 1565 Dihedral : 4.680 60.354 1265 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.87 % Allowed : 18.45 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1133 helix: 0.70 (0.26), residues: 415 sheet: -0.34 (0.29), residues: 283 loop : -0.81 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.015 0.001 TYR E 190 PHE 0.011 0.001 PHE B 235 TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9225) covalent geometry : angle 0.53604 (12486) SS BOND : bond 0.00284 ( 3) SS BOND : angle 0.65951 ( 6) hydrogen bonds : bond 0.03462 ( 427) hydrogen bonds : angle 4.74426 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.248 Fit side-chains REVERT: A 10 LYS cc_start: 0.8329 (mtmm) cc_final: 0.8102 (mtmm) REVERT: A 18 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8204 (mtm) REVERT: A 32 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7957 (ttm-80) REVERT: A 186 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 197 LYS cc_start: 0.8341 (mttt) cc_final: 0.8022 (mttp) REVERT: A 209 LYS cc_start: 0.8074 (ttpp) cc_final: 0.7813 (ttpp) REVERT: A 210 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8239 (mmtt) REVERT: A 245 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 271 LYS cc_start: 0.8804 (pttt) cc_final: 0.8499 (pttp) REVERT: A 283 LEU cc_start: 0.8648 (tp) cc_final: 0.8334 (tm) REVERT: A 309 ASP cc_start: 0.7750 (m-30) cc_final: 0.7360 (m-30) REVERT: A 318 GLU cc_start: 0.7514 (tp30) cc_final: 0.7301 (tp30) REVERT: B 38 ASP cc_start: 0.8372 (m-30) cc_final: 0.8133 (m-30) REVERT: B 45 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: B 132 ASN cc_start: 0.8261 (p0) cc_final: 0.8030 (p0) REVERT: B 147 SER cc_start: 0.8529 (m) cc_final: 0.8118 (p) REVERT: B 150 ARG cc_start: 0.8830 (mmt-90) cc_final: 0.8510 (mpt180) REVERT: B 217 MET cc_start: 0.7805 (mmm) cc_final: 0.7554 (mmm) REVERT: B 312 ASP cc_start: 0.7973 (m-30) cc_final: 0.7630 (m-30) REVERT: E 25 SER cc_start: 0.8504 (t) cc_final: 0.8288 (p) REVERT: E 67 ARG cc_start: 0.8540 (mtm110) cc_final: 0.8292 (mtm-85) REVERT: E 84 THR cc_start: 0.8500 (m) cc_final: 0.8073 (p) REVERT: E 85 SER cc_start: 0.8704 (m) cc_final: 0.8495 (p) REVERT: E 186 GLN cc_start: 0.8475 (pt0) cc_final: 0.8162 (pt0) REVERT: E 191 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6570 (mtp180) REVERT: E 210 THR cc_start: 0.8013 (p) cc_final: 0.7723 (m) REVERT: R 41 VAL cc_start: 0.8506 (t) cc_final: 0.8186 (p) REVERT: R 56 THR cc_start: 0.8685 (t) cc_final: 0.8363 (p) REVERT: R 58 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7876 (p) REVERT: R 69 LEU cc_start: 0.8465 (mp) cc_final: 0.8214 (mp) REVERT: R 137 ARG cc_start: 0.8594 (ttt-90) cc_final: 0.8203 (ttt90) REVERT: R 164 LEU cc_start: 0.8401 (tt) cc_final: 0.7902 (tm) REVERT: R 165 THR cc_start: 0.8383 (t) cc_final: 0.8038 (p) REVERT: R 201 ARG cc_start: 0.8029 (ttt90) cc_final: 0.7655 (ttt-90) REVERT: R 250 PHE cc_start: 0.8313 (t80) cc_final: 0.7745 (t80) REVERT: R 266 VAL cc_start: 0.8231 (t) cc_final: 0.7895 (m) REVERT: R 283 LEU cc_start: 0.8090 (mt) cc_final: 0.7835 (mt) REVERT: R 284 VAL cc_start: 0.8026 (p) cc_final: 0.7756 (t) REVERT: R 288 SER cc_start: 0.8361 (p) cc_final: 0.8140 (m) outliers start: 38 outliers final: 18 residues processed: 239 average time/residue: 0.6206 time to fit residues: 157.4815 Evaluate side-chains 236 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 220 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099929 restraints weight = 12653.380| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.74 r_work: 0.3191 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9228 Z= 0.137 Angle : 0.538 10.957 12492 Z= 0.278 Chirality : 0.042 0.136 1422 Planarity : 0.004 0.043 1565 Dihedral : 4.641 59.336 1265 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.77 % Allowed : 19.16 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.25), residues: 1133 helix: 0.91 (0.27), residues: 417 sheet: -0.26 (0.30), residues: 282 loop : -0.68 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 54 TYR 0.015 0.001 TYR E 190 PHE 0.023 0.001 PHE E 68 TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9225) covalent geometry : angle 0.53845 (12486) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.62209 ( 6) hydrogen bonds : bond 0.03435 ( 427) hydrogen bonds : angle 4.65506 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.409 Fit side-chains REVERT: A 10 LYS cc_start: 0.8327 (mtmm) cc_final: 0.8084 (mtmm) REVERT: A 18 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8246 (mtm) REVERT: A 32 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.8013 (ttm-80) REVERT: A 186 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 197 LYS cc_start: 0.8353 (mttt) cc_final: 0.8025 (mttp) REVERT: A 209 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7811 (ttpp) REVERT: A 210 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8214 (mmtt) REVERT: A 245 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 251 ASP cc_start: 0.7899 (t0) cc_final: 0.7653 (t0) REVERT: A 271 LYS cc_start: 0.8797 (pttt) cc_final: 0.8483 (pttp) REVERT: A 283 LEU cc_start: 0.8652 (tp) cc_final: 0.8337 (tm) REVERT: A 309 ASP cc_start: 0.7747 (m-30) cc_final: 0.7334 (m-30) REVERT: A 318 GLU cc_start: 0.7509 (tp30) cc_final: 0.7285 (tp30) REVERT: B 38 ASP cc_start: 0.8333 (m-30) cc_final: 0.8095 (m-30) REVERT: B 45 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8346 (mtm) REVERT: B 49 ARG cc_start: 0.8704 (mmt90) cc_final: 0.8405 (tpp-160) REVERT: B 132 ASN cc_start: 0.8241 (p0) cc_final: 0.8011 (p0) REVERT: B 147 SER cc_start: 0.8553 (m) cc_final: 0.8135 (p) REVERT: B 150 ARG cc_start: 0.8828 (mmt-90) cc_final: 0.8495 (mpt180) REVERT: B 217 MET cc_start: 0.7759 (mmm) cc_final: 0.7516 (mmm) REVERT: B 312 ASP cc_start: 0.7930 (m-30) cc_final: 0.7606 (m-30) REVERT: E 25 SER cc_start: 0.8509 (t) cc_final: 0.8278 (p) REVERT: E 67 ARG cc_start: 0.8533 (mtm110) cc_final: 0.8324 (mtm-85) REVERT: E 84 THR cc_start: 0.8495 (m) cc_final: 0.8067 (p) REVERT: E 85 SER cc_start: 0.8688 (m) cc_final: 0.8444 (p) REVERT: E 186 GLN cc_start: 0.8469 (pt0) cc_final: 0.8240 (pt0) REVERT: E 191 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.6537 (mtp180) REVERT: E 210 THR cc_start: 0.7995 (p) cc_final: 0.7714 (m) REVERT: R 56 THR cc_start: 0.8645 (t) cc_final: 0.8349 (p) REVERT: R 58 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7904 (p) REVERT: R 69 LEU cc_start: 0.8425 (mp) cc_final: 0.8168 (mp) REVERT: R 137 ARG cc_start: 0.8596 (ttt-90) cc_final: 0.8215 (ttt90) REVERT: R 165 THR cc_start: 0.8376 (t) cc_final: 0.8026 (p) REVERT: R 250 PHE cc_start: 0.8273 (t80) cc_final: 0.7742 (t80) REVERT: R 266 VAL cc_start: 0.8216 (t) cc_final: 0.7884 (m) REVERT: R 283 LEU cc_start: 0.8102 (mt) cc_final: 0.7826 (mt) REVERT: R 284 VAL cc_start: 0.8035 (p) cc_final: 0.7768 (t) REVERT: R 288 SER cc_start: 0.8377 (p) cc_final: 0.8162 (m) REVERT: R 310 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7586 (mtm110) outliers start: 37 outliers final: 21 residues processed: 237 average time/residue: 0.6505 time to fit residues: 163.3995 Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 0.0000 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 155 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102812 restraints weight = 12548.055| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.76 r_work: 0.3163 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9228 Z= 0.156 Angle : 0.551 12.069 12492 Z= 0.285 Chirality : 0.043 0.133 1422 Planarity : 0.004 0.043 1565 Dihedral : 4.701 59.524 1265 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.87 % Allowed : 19.67 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1133 helix: 1.10 (0.27), residues: 411 sheet: -0.12 (0.30), residues: 275 loop : -0.66 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 202 TYR 0.014 0.001 TYR E 190 PHE 0.019 0.001 PHE E 68 TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9225) covalent geometry : angle 0.55088 (12486) SS BOND : bond 0.00301 ( 3) SS BOND : angle 0.69994 ( 6) hydrogen bonds : bond 0.03546 ( 427) hydrogen bonds : angle 4.67744 ( 1218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 219 time to evaluate : 0.349 Fit side-chains REVERT: A 10 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8099 (mtmm) REVERT: A 18 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8279 (mtm) REVERT: A 32 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7939 (ttm-80) REVERT: A 186 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 197 LYS cc_start: 0.8362 (mttt) cc_final: 0.8017 (mttp) REVERT: A 209 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7802 (ttpp) REVERT: A 210 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8225 (mmtt) REVERT: A 245 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7498 (mm-30) REVERT: A 251 ASP cc_start: 0.7890 (t0) cc_final: 0.7636 (t0) REVERT: A 271 LYS cc_start: 0.8795 (pttt) cc_final: 0.8470 (pttp) REVERT: A 283 LEU cc_start: 0.8626 (tp) cc_final: 0.8301 (tm) REVERT: A 309 ASP cc_start: 0.7727 (m-30) cc_final: 0.7290 (m-30) REVERT: A 317 LYS cc_start: 0.8336 (ptpp) cc_final: 0.8125 (ptpt) REVERT: A 318 GLU cc_start: 0.7526 (tp30) cc_final: 0.7307 (tp30) REVERT: A 329 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7750 (m) REVERT: B 38 ASP cc_start: 0.8364 (m-30) cc_final: 0.8124 (m-30) REVERT: B 45 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8371 (mtm) REVERT: B 49 ARG cc_start: 0.8705 (mmt90) cc_final: 0.8396 (tpp-160) REVERT: B 132 ASN cc_start: 0.8249 (p0) cc_final: 0.8011 (p0) REVERT: B 147 SER cc_start: 0.8556 (m) cc_final: 0.8059 (p) REVERT: B 150 ARG cc_start: 0.8825 (mmt-90) cc_final: 0.8494 (mpt180) REVERT: B 163 ASP cc_start: 0.7391 (p0) cc_final: 0.7014 (p0) REVERT: B 217 MET cc_start: 0.7792 (mmm) cc_final: 0.7545 (mmm) REVERT: B 312 ASP cc_start: 0.7953 (m-30) cc_final: 0.7631 (m-30) REVERT: E 25 SER cc_start: 0.8518 (t) cc_final: 0.8264 (p) REVERT: E 67 ARG cc_start: 0.8502 (mtm110) cc_final: 0.8268 (mtm-85) REVERT: E 68 PHE cc_start: 0.8277 (m-10) cc_final: 0.7958 (m-10) REVERT: E 84 THR cc_start: 0.8479 (m) cc_final: 0.8014 (p) REVERT: E 85 SER cc_start: 0.8696 (m) cc_final: 0.8460 (p) REVERT: E 186 GLN cc_start: 0.8464 (pt0) cc_final: 0.8138 (pt0) REVERT: E 210 THR cc_start: 0.7999 (p) cc_final: 0.7704 (m) REVERT: R 56 THR cc_start: 0.8662 (t) cc_final: 0.8371 (p) REVERT: R 69 LEU cc_start: 0.8424 (mp) cc_final: 0.8168 (mp) REVERT: R 137 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.8213 (ttt90) REVERT: R 165 THR cc_start: 0.8369 (t) cc_final: 0.8006 (p) REVERT: R 250 PHE cc_start: 0.8306 (t80) cc_final: 0.7737 (t80) REVERT: R 266 VAL cc_start: 0.8206 (t) cc_final: 0.7854 (m) REVERT: R 283 LEU cc_start: 0.8113 (mt) cc_final: 0.7837 (mt) REVERT: R 284 VAL cc_start: 0.7998 (p) cc_final: 0.7743 (t) REVERT: R 288 SER cc_start: 0.8353 (p) cc_final: 0.8140 (m) outliers start: 38 outliers final: 27 residues processed: 239 average time/residue: 0.6457 time to fit residues: 163.7567 Evaluate side-chains 248 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 199 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 30 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 155 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101544 restraints weight = 12541.417| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.72 r_work: 0.3211 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9228 Z= 0.116 Angle : 0.533 11.287 12492 Z= 0.275 Chirality : 0.042 0.137 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.588 59.042 1265 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.77 % Allowed : 20.08 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1133 helix: 1.26 (0.27), residues: 411 sheet: -0.11 (0.30), residues: 271 loop : -0.62 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 310 TYR 0.014 0.001 TYR E 190 PHE 0.023 0.001 PHE R 163 TRP 0.014 0.001 TRP B 211 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9225) covalent geometry : angle 0.53267 (12486) SS BOND : bond 0.00242 ( 3) SS BOND : angle 0.54662 ( 6) hydrogen bonds : bond 0.03296 ( 427) hydrogen bonds : angle 4.60742 ( 1218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.353 Fit side-chains REVERT: A 10 LYS cc_start: 0.8253 (mtmm) cc_final: 0.8016 (mtmm) REVERT: A 18 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8246 (mtm) REVERT: A 186 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 197 LYS cc_start: 0.8374 (mttt) cc_final: 0.8046 (mttp) REVERT: A 209 LYS cc_start: 0.7992 (ttpp) cc_final: 0.7784 (ttpp) REVERT: A 210 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8201 (mmtt) REVERT: A 245 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 251 ASP cc_start: 0.7878 (t0) cc_final: 0.7645 (t0) REVERT: A 271 LYS cc_start: 0.8798 (pttt) cc_final: 0.8471 (pttp) REVERT: A 283 LEU cc_start: 0.8656 (tp) cc_final: 0.8358 (tm) REVERT: A 309 ASP cc_start: 0.7696 (m-30) cc_final: 0.7256 (m-30) REVERT: A 317 LYS cc_start: 0.8326 (ptpp) cc_final: 0.8116 (ptpt) REVERT: A 318 GLU cc_start: 0.7500 (tp30) cc_final: 0.7277 (tp30) REVERT: A 329 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7703 (m) REVERT: B 38 ASP cc_start: 0.8346 (m-30) cc_final: 0.8119 (m-30) REVERT: B 45 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8339 (mtm) REVERT: B 49 ARG cc_start: 0.8685 (mmt90) cc_final: 0.8410 (tpp-160) REVERT: B 132 ASN cc_start: 0.8234 (p0) cc_final: 0.7998 (p0) REVERT: B 147 SER cc_start: 0.8537 (m) cc_final: 0.8193 (p) REVERT: B 150 ARG cc_start: 0.8827 (mmt-90) cc_final: 0.8479 (mpt180) REVERT: B 217 MET cc_start: 0.7748 (mmm) cc_final: 0.7508 (mmm) REVERT: B 312 ASP cc_start: 0.7944 (m-30) cc_final: 0.7622 (m-30) REVERT: E 25 SER cc_start: 0.8514 (t) cc_final: 0.8288 (p) REVERT: E 68 PHE cc_start: 0.8235 (m-10) cc_final: 0.7910 (m-10) REVERT: E 84 THR cc_start: 0.8500 (m) cc_final: 0.8063 (p) REVERT: E 85 SER cc_start: 0.8680 (m) cc_final: 0.8395 (p) REVERT: E 141 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8483 (p) REVERT: E 186 GLN cc_start: 0.8449 (pt0) cc_final: 0.8129 (pt0) REVERT: E 191 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.6534 (mtp180) REVERT: E 210 THR cc_start: 0.7971 (p) cc_final: 0.7720 (m) REVERT: R 56 THR cc_start: 0.8642 (t) cc_final: 0.8334 (p) REVERT: R 58 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7891 (p) REVERT: R 69 LEU cc_start: 0.8418 (mp) cc_final: 0.8185 (mp) REVERT: R 137 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.8224 (ttt90) REVERT: R 165 THR cc_start: 0.8349 (t) cc_final: 0.8003 (p) REVERT: R 197 MET cc_start: 0.6906 (tmm) cc_final: 0.6699 (tmm) REVERT: R 250 PHE cc_start: 0.8219 (t80) cc_final: 0.7668 (t80) REVERT: R 266 VAL cc_start: 0.8235 (t) cc_final: 0.7876 (m) REVERT: R 283 LEU cc_start: 0.8120 (mt) cc_final: 0.7812 (mt) REVERT: R 284 VAL cc_start: 0.8004 (p) cc_final: 0.7739 (t) outliers start: 37 outliers final: 23 residues processed: 231 average time/residue: 0.5988 time to fit residues: 147.1828 Evaluate side-chains 237 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 155 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100641 restraints weight = 12598.431| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.72 r_work: 0.3173 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9228 Z= 0.158 Angle : 0.569 10.549 12492 Z= 0.291 Chirality : 0.043 0.139 1422 Planarity : 0.004 0.076 1565 Dihedral : 4.671 59.291 1265 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.47 % Allowed : 21.00 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1133 helix: 1.21 (0.27), residues: 411 sheet: -0.04 (0.30), residues: 281 loop : -0.62 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 32 TYR 0.014 0.001 TYR B 111 PHE 0.016 0.001 PHE R 93 TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9225) covalent geometry : angle 0.56867 (12486) SS BOND : bond 0.00297 ( 3) SS BOND : angle 0.63597 ( 6) hydrogen bonds : bond 0.03504 ( 427) hydrogen bonds : angle 4.65029 ( 1218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.355 Fit side-chains REVERT: A 10 LYS cc_start: 0.8293 (mtmm) cc_final: 0.8041 (mtmm) REVERT: A 18 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8251 (mtm) REVERT: A 186 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 197 LYS cc_start: 0.8388 (mttt) cc_final: 0.8040 (mttp) REVERT: A 209 LYS cc_start: 0.8025 (ttpp) cc_final: 0.7798 (ttpp) REVERT: A 210 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8224 (mmtt) REVERT: A 245 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 251 ASP cc_start: 0.7882 (t0) cc_final: 0.7633 (t0) REVERT: A 271 LYS cc_start: 0.8782 (pttt) cc_final: 0.8462 (pttp) REVERT: A 283 LEU cc_start: 0.8609 (tp) cc_final: 0.8302 (tm) REVERT: A 309 ASP cc_start: 0.7719 (m-30) cc_final: 0.7277 (m-30) REVERT: A 318 GLU cc_start: 0.7505 (tp30) cc_final: 0.7285 (tp30) REVERT: A 329 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7766 (m) REVERT: B 38 ASP cc_start: 0.8376 (m-30) cc_final: 0.8142 (m-30) REVERT: B 45 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8360 (mtm) REVERT: B 49 ARG cc_start: 0.8702 (mmt90) cc_final: 0.8410 (tpp-160) REVERT: B 132 ASN cc_start: 0.8231 (p0) cc_final: 0.8002 (p0) REVERT: B 147 SER cc_start: 0.8543 (m) cc_final: 0.8013 (p) REVERT: B 150 ARG cc_start: 0.8844 (mmt-90) cc_final: 0.8513 (mpt180) REVERT: B 217 MET cc_start: 0.7752 (mmm) cc_final: 0.7518 (mmm) REVERT: B 312 ASP cc_start: 0.7965 (m-30) cc_final: 0.7646 (m-30) REVERT: E 25 SER cc_start: 0.8524 (t) cc_final: 0.8279 (p) REVERT: E 67 ARG cc_start: 0.8510 (mtm110) cc_final: 0.8294 (mtm-85) REVERT: E 68 PHE cc_start: 0.8239 (m-10) cc_final: 0.7872 (m-10) REVERT: E 84 THR cc_start: 0.8502 (m) cc_final: 0.8028 (p) REVERT: E 85 SER cc_start: 0.8683 (m) cc_final: 0.8458 (p) REVERT: E 141 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8493 (p) REVERT: E 186 GLN cc_start: 0.8455 (pt0) cc_final: 0.8132 (pt0) REVERT: E 191 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.6579 (mtp180) REVERT: E 210 THR cc_start: 0.8041 (p) cc_final: 0.7773 (m) REVERT: R 56 THR cc_start: 0.8646 (t) cc_final: 0.8342 (p) REVERT: R 58 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7913 (p) REVERT: R 69 LEU cc_start: 0.8420 (mp) cc_final: 0.8153 (mp) REVERT: R 137 ARG cc_start: 0.8616 (ttt-90) cc_final: 0.8238 (ttt90) REVERT: R 164 LEU cc_start: 0.8335 (tt) cc_final: 0.7894 (tp) REVERT: R 165 THR cc_start: 0.8341 (t) cc_final: 0.7945 (p) REVERT: R 250 PHE cc_start: 0.8267 (t80) cc_final: 0.7733 (t80) REVERT: R 266 VAL cc_start: 0.8214 (t) cc_final: 0.7848 (m) REVERT: R 283 LEU cc_start: 0.8110 (mt) cc_final: 0.7813 (mt) REVERT: R 284 VAL cc_start: 0.7952 (p) cc_final: 0.7710 (t) outliers start: 34 outliers final: 21 residues processed: 233 average time/residue: 0.6400 time to fit residues: 158.0288 Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 85 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 155 ASN B 237 ASN B 259 GLN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100919 restraints weight = 12469.069| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.71 r_work: 0.3199 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9228 Z= 0.140 Angle : 0.564 12.560 12492 Z= 0.288 Chirality : 0.043 0.137 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.636 59.132 1265 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.16 % Allowed : 21.00 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.25), residues: 1133 helix: 1.27 (0.27), residues: 411 sheet: -0.03 (0.30), residues: 281 loop : -0.61 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 310 TYR 0.015 0.001 TYR B 111 PHE 0.026 0.001 PHE R 163 TRP 0.013 0.001 TRP B 169 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9225) covalent geometry : angle 0.56421 (12486) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.59433 ( 6) hydrogen bonds : bond 0.03420 ( 427) hydrogen bonds : angle 4.63541 ( 1218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.341 Fit side-chains REVERT: A 10 LYS cc_start: 0.8264 (mtmm) cc_final: 0.8029 (mtmm) REVERT: A 18 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8254 (mtm) REVERT: A 32 ARG cc_start: 0.8191 (ttm-80) cc_final: 0.7960 (ttm-80) REVERT: A 186 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 197 LYS cc_start: 0.8378 (mttt) cc_final: 0.8058 (mttp) REVERT: A 209 LYS cc_start: 0.7996 (ttpp) cc_final: 0.7791 (ttpp) REVERT: A 210 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8221 (mmtt) REVERT: A 232 LEU cc_start: 0.8653 (mm) cc_final: 0.8280 (mp) REVERT: A 245 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 251 ASP cc_start: 0.7862 (t0) cc_final: 0.7640 (t0) REVERT: A 271 LYS cc_start: 0.8794 (pttt) cc_final: 0.8478 (pttp) REVERT: A 283 LEU cc_start: 0.8626 (tp) cc_final: 0.8328 (tm) REVERT: A 309 ASP cc_start: 0.7704 (m-30) cc_final: 0.7268 (m-30) REVERT: A 318 GLU cc_start: 0.7499 (tp30) cc_final: 0.7272 (tp30) REVERT: A 329 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7769 (m) REVERT: B 38 ASP cc_start: 0.8362 (m-30) cc_final: 0.8127 (m-30) REVERT: B 45 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8343 (mtm) REVERT: B 49 ARG cc_start: 0.8663 (mmt90) cc_final: 0.8442 (tpp-160) REVERT: B 132 ASN cc_start: 0.8239 (p0) cc_final: 0.7992 (p0) REVERT: B 147 SER cc_start: 0.8512 (m) cc_final: 0.8043 (p) REVERT: B 150 ARG cc_start: 0.8849 (mmt-90) cc_final: 0.8515 (mpt180) REVERT: B 155 ASN cc_start: 0.8045 (t0) cc_final: 0.7661 (t0) REVERT: B 217 MET cc_start: 0.7727 (mmm) cc_final: 0.7495 (mmm) REVERT: B 312 ASP cc_start: 0.7946 (m-30) cc_final: 0.7634 (m-30) REVERT: E 25 SER cc_start: 0.8525 (t) cc_final: 0.8296 (p) REVERT: E 68 PHE cc_start: 0.8221 (m-10) cc_final: 0.7865 (m-10) REVERT: E 84 THR cc_start: 0.8510 (m) cc_final: 0.8058 (p) REVERT: E 85 SER cc_start: 0.8685 (m) cc_final: 0.8419 (p) REVERT: E 141 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8520 (p) REVERT: E 186 GLN cc_start: 0.8450 (pt0) cc_final: 0.8125 (pt0) REVERT: E 191 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.6583 (mtp180) REVERT: E 210 THR cc_start: 0.8033 (p) cc_final: 0.7777 (m) REVERT: R 56 THR cc_start: 0.8652 (t) cc_final: 0.8339 (p) REVERT: R 58 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7938 (p) REVERT: R 69 LEU cc_start: 0.8425 (mp) cc_final: 0.8184 (mp) REVERT: R 137 ARG cc_start: 0.8630 (ttt-90) cc_final: 0.8261 (ttt90) REVERT: R 164 LEU cc_start: 0.8304 (tt) cc_final: 0.8067 (tp) REVERT: R 250 PHE cc_start: 0.8238 (t80) cc_final: 0.7736 (t80) REVERT: R 266 VAL cc_start: 0.8231 (t) cc_final: 0.7880 (m) REVERT: R 283 LEU cc_start: 0.8162 (mt) cc_final: 0.7890 (mt) REVERT: R 284 VAL cc_start: 0.7975 (p) cc_final: 0.7739 (t) outliers start: 31 outliers final: 23 residues processed: 226 average time/residue: 0.5991 time to fit residues: 144.0822 Evaluate side-chains 231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 161 PHE Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 186 THR Chi-restraints excluded: chain R residue 241 ARG Chi-restraints excluded: chain R residue 274 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 237 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098741 restraints weight = 12576.019| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.78 r_work: 0.3175 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9228 Z= 0.132 Angle : 0.564 14.067 12492 Z= 0.286 Chirality : 0.043 0.140 1422 Planarity : 0.004 0.042 1565 Dihedral : 4.615 58.953 1265 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.47 % Allowed : 21.00 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.25), residues: 1133 helix: 1.30 (0.27), residues: 411 sheet: 0.05 (0.30), residues: 291 loop : -0.59 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 54 TYR 0.015 0.001 TYR B 111 PHE 0.018 0.001 PHE R 93 TRP 0.013 0.001 TRP B 211 HIS 0.010 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9225) covalent geometry : angle 0.56383 (12486) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.57538 ( 6) hydrogen bonds : bond 0.03375 ( 427) hydrogen bonds : angle 4.61175 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3772.12 seconds wall clock time: 64 minutes 54.64 seconds (3894.64 seconds total)