Starting phenix.real_space_refine on Fri Sep 11 16:30:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xbj_22117/09_2026/6xbj_22117.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 76 5.16 5 C 6481 2.51 5 N 1735 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10198 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3658 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain breaks: 1 Chain: "A" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1736 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.20 Number of scatterers: 10198 At special positions: 0 Unit cell: (109.956, 124.117, 163.268, 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 76 16.00 O 1906 8.00 N 1735 7.00 C 6481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS R 64 " - pdb=" SG CYS R 178 " distance=2.03 Simple disulfide: pdb=" SG CYS R 70 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 127 " distance=2.03 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 154 " distance=2.03 Simple disulfide: pdb=" SG CYS R 147 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 213 " distance=2.03 Simple disulfide: pdb=" SG CYS R 217 " - pdb=" SG CYS R 295 " distance=2.03 Simple disulfide: pdb=" SG CYS R 314 " - pdb=" SG CYS R 390 " distance=2.03 Simple disulfide: pdb=" SG CYS R 490 " - pdb=" SG CYS R 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 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: 0.93 Conformation dependent library (CDL) restraints added in 363.8 milliseconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 36.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 98 through 110 Processing helix chain 'R' and resid 111 through 114 removed outlier: 4.293A pdb=" N ASN R 114 " --> pdb=" O GLY R 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 111 through 114' Processing helix chain 'R' and resid 115 through 130 removed outlier: 4.384A pdb=" N VAL R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 143 through 150 removed outlier: 3.975A pdb=" N CYS R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR R 150 " --> pdb=" O LEU R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 161 removed outlier: 4.162A pdb=" N ARG R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 185 removed outlier: 3.659A pdb=" N ASN R 184 " --> pdb=" O GLU R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 206 removed outlier: 3.926A pdb=" N TRP R 206 " --> pdb=" O PRO R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 255 removed outlier: 3.936A pdb=" N ASP R 255 " --> pdb=" O THR R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 282 Processing helix chain 'R' and resid 289 through 294 Processing helix chain 'R' and resid 314 through 345 removed outlier: 3.730A pdb=" N ALA R 345 " --> pdb=" O THR R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 355 removed outlier: 3.895A pdb=" N GLY R 355 " --> pdb=" O PRO R 352 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 378 Proline residue: R 368 - end of helix Processing helix chain 'R' and resid 396 through 429 removed outlier: 4.135A pdb=" N ARG R 400 " --> pdb=" O ASN R 396 " (cutoff:3.500A) Proline residue: R 407 - end of helix Processing helix chain 'R' and resid 438 through 494 removed outlier: 3.568A pdb=" N LYS R 444 " --> pdb=" O LYS R 440 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE R 455 " --> pdb=" O ARG R 451 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE R 460 " --> pdb=" O GLY R 456 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL R 463 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR R 466 " --> pdb=" O PHE R 462 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP R 473 " --> pdb=" O CYS R 469 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN R 476 " --> pdb=" O TYR R 472 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA R 478 " --> pdb=" O PHE R 474 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU R 479 " --> pdb=" O PHE R 475 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL R 494 " --> pdb=" O CYS R 490 " (cutoff:3.500A) Processing helix chain 'R' and resid 514 through 532 removed outlier: 4.147A pdb=" N GLU R 518 " --> pdb=" O SER R 514 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET R 532 " --> pdb=" O THR R 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.662A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.961A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.003A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.626A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.028A 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 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.762A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 29 through 36 removed outlier: 4.178A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.877A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.908A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, first strand: chain 'R' and resid 197 through 199 Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.529A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.854A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.117A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.846A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.575A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 191 removed outlier: 5.349A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.687A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.451A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.843A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.576A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.576A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.454A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147 removed outlier: 3.642A pdb=" N ILE S 145 " --> pdb=" O LEU S 202 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR S 201 " --> pdb=" O SER S 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 182 through 183 removed outlier: 6.914A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1984 1.33 - 1.46: 2601 1.46 - 1.58: 5737 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 10427 Sorted by residual: bond pdb=" N VAL S 64 " pdb=" CA VAL S 64 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.04e-02 9.25e+03 1.66e+01 bond pdb=" N VAL B 90 " pdb=" CA VAL B 90 " ideal model delta sigma weight residual 1.452 1.497 -0.045 1.18e-02 7.18e+03 1.46e+01 bond pdb=" N VAL R 404 " pdb=" CA VAL R 404 " ideal model delta sigma weight residual 1.452 1.497 -0.044 1.18e-02 7.18e+03 1.42e+01 bond pdb=" N LEU R 367 " pdb=" CA LEU R 367 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N GLY B 185 " pdb=" CA GLY B 185 " ideal model delta sigma weight residual 1.445 1.478 -0.034 9.20e-03 1.18e+04 1.33e+01 ... (remaining 10422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 9825 1.85 - 3.70: 3796 3.70 - 5.56: 491 5.56 - 7.41: 20 7.41 - 9.26: 2 Bond angle restraints: 14134 Sorted by residual: angle pdb=" C TYR S 223 " pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " ideal model delta sigma weight residual 110.34 101.08 9.26 1.30e+00 5.92e-01 5.07e+01 angle pdb=" C GLN R 216 " pdb=" N CYS R 217 " pdb=" CA CYS R 217 " ideal model delta sigma weight residual 120.28 127.65 -7.37 1.34e+00 5.57e-01 3.03e+01 angle pdb=" C GLU R 194 " pdb=" N VAL R 195 " pdb=" CA VAL R 195 " ideal model delta sigma weight residual 120.43 125.32 -4.89 9.60e-01 1.09e+00 2.60e+01 angle pdb=" C GLY R 415 " pdb=" N GLY R 416 " pdb=" CA GLY R 416 " ideal model delta sigma weight residual 119.99 125.40 -5.41 1.13e+00 7.83e-01 2.29e+01 angle pdb=" C PHE A 259 " pdb=" N THR A 260 " pdb=" CA THR A 260 " ideal model delta sigma weight residual 120.38 126.90 -6.52 1.37e+00 5.33e-01 2.26e+01 ... (remaining 14129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.29: 5878 25.29 - 50.58: 272 50.58 - 75.87: 19 75.87 - 101.16: 0 101.16 - 126.45: 1 Dihedral angle restraints: 6170 sinusoidal: 2423 harmonic: 3747 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 53.55 126.45 0 5.00e+00 4.00e-02 6.40e+02 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.74 -66.74 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS R 217 " pdb=" SG CYS R 217 " pdb=" SG CYS R 295 " pdb=" CB CYS R 295 " ideal model delta sinusoidal sigma weight residual -86.00 -137.69 51.69 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 6167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 720 0.057 - 0.115: 587 0.115 - 0.172: 244 0.172 - 0.229: 20 0.229 - 0.286: 1 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C14 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C15 CLR R 701 " pdb=" C8 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TYR R 262 " pdb=" N TYR R 262 " pdb=" C TYR R 262 " pdb=" CB TYR R 262 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1569 not shown) Planarity restraints: 1801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.95e+00 pdb=" N PRO S 224 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 121 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C CYS B 121 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS B 121 " 0.018 2.00e-02 2.50e+03 pdb=" N SER B 122 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 259 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C PHE A 259 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE A 259 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 260 " 0.013 2.00e-02 2.50e+03 ... (remaining 1798 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 320 2.71 - 3.26: 10019 3.26 - 3.81: 15273 3.81 - 4.35: 19567 4.35 - 4.90: 33005 Nonbonded interactions: 78184 Sorted by model distance: nonbonded pdb=" O MET R 525 " pdb=" OG1 THR R 528 " model vdw 2.168 3.040 nonbonded pdb=" O ILE R 375 " pdb=" O VAL R 378 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.314 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.342 3.040 ... (remaining 78179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 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 : 0.014 0.060 10439 Z= 1.063 Angle : 1.762 9.259 14158 Z= 1.292 Chirality : 0.082 0.286 1572 Planarity : 0.004 0.079 1801 Dihedral : 13.694 126.448 3726 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.36 % Allowed : 5.99 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: -4.02 (0.19), residues: 1283 helix: -1.62 (0.22), residues: 411 sheet: -3.57 (0.28), residues: 216 loop : -3.08 (0.20), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 179 TYR 0.024 0.003 TYR S 103 PHE 0.019 0.003 PHE A 334 TRP 0.026 0.002 TRP R 163 HIS 0.008 0.002 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.01385 / 1.06 (10427) covalent geometry : angle 1.76164 / 1.29 (14134) SS BOND : bond 0.00872 / 0.78 ( 12) SS BOND : angle 1.79534 / 1.27 ( 24) hydrogen bonds : bond 0.23048 / 15.24 ( 428) hydrogen bonds : angle 8.27082 / 5.79 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 287 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 74 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6766 (tpt90) REVERT: R 237 PHE cc_start: 0.7163 (t80) cc_final: 0.6641 (t80) REVERT: R 261 ARG cc_start: 0.5099 (ptt-90) cc_final: 0.4857 (ptt-90) REVERT: R 301 MET cc_start: 0.8609 (ptp) cc_final: 0.8054 (ptp) REVERT: R 339 TRP cc_start: 0.7367 (m-10) cc_final: 0.6973 (m-10) REVERT: R 381 VAL cc_start: 0.6174 (OUTLIER) cc_final: 0.5743 (p) REVERT: R 397 TYR cc_start: 0.7588 (p90) cc_final: 0.7375 (p90) REVERT: R 424 MET cc_start: 0.8881 (mtm) cc_final: 0.8570 (mtm) REVERT: R 439 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7703 (tp30) REVERT: R 473 ASP cc_start: 0.8618 (t0) cc_final: 0.8351 (t0) REVERT: R 475 PHE cc_start: 0.5459 (m-80) cc_final: 0.4983 (m-10) REVERT: R 480 TRP cc_start: 0.7432 (m-10) cc_final: 0.7113 (m-90) REVERT: R 482 ARG cc_start: 0.7839 (tmm-80) cc_final: 0.7398 (mpt180) REVERT: R 486 ASP cc_start: 0.8086 (m-30) cc_final: 0.7376 (m-30) REVERT: R 526 PHE cc_start: 0.7629 (m-10) cc_final: 0.7420 (m-80) REVERT: R 532 MET cc_start: 0.7814 (mmt) cc_final: 0.7546 (mmt) REVERT: A 8 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7953 (mt-10) REVERT: A 200 ASP cc_start: 0.7996 (p0) cc_final: 0.7552 (t0) REVERT: A 242 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.6900 (mmt180) REVERT: A 243 MET cc_start: 0.7368 (tpp) cc_final: 0.7048 (tpp) REVERT: A 275 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8335 (tt0) REVERT: A 277 LYS cc_start: 0.8117 (tptt) cc_final: 0.7812 (tppt) REVERT: A 302 TYR cc_start: 0.7625 (t80) cc_final: 0.7194 (t80) REVERT: B 20 ASP cc_start: 0.8974 (t0) cc_final: 0.8771 (t0) REVERT: B 36 ASN cc_start: 0.8418 (t0) cc_final: 0.8186 (t0) REVERT: B 37 ILE cc_start: 0.8993 (tp) cc_final: 0.8644 (tp) REVERT: B 95 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7484 (pp) REVERT: B 138 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7381 (pp20) REVERT: B 188 MET cc_start: 0.8194 (mmm) cc_final: 0.7953 (mmm) REVERT: B 189 SER cc_start: 0.8613 (t) cc_final: 0.8298 (t) REVERT: B 215 GLU cc_start: 0.8196 (mp0) cc_final: 0.7445 (mp0) REVERT: B 217 MET cc_start: 0.7107 (ptp) cc_final: 0.6887 (ptp) REVERT: B 228 ASP cc_start: 0.7689 (m-30) cc_final: 0.6515 (m-30) REVERT: B 260 GLU cc_start: 0.8671 (tt0) cc_final: 0.8138 (tt0) REVERT: B 284 LEU cc_start: 0.7605 (pt) cc_final: 0.7235 (pt) REVERT: B 295 ASN cc_start: 0.8514 (m-40) cc_final: 0.8136 (m-40) REVERT: B 297 TRP cc_start: 0.8319 (m100) cc_final: 0.7691 (m100) REVERT: B 325 MET cc_start: 0.8160 (mmm) cc_final: 0.7791 (tpt) REVERT: B 339 TRP cc_start: 0.8243 (m100) cc_final: 0.7772 (m100) REVERT: G 18 GLN cc_start: 0.6855 (tm-30) cc_final: 0.6006 (tm-30) REVERT: G 21 MET cc_start: 0.7900 (ttp) cc_final: 0.7507 (tmm) REVERT: G 38 MET cc_start: 0.7914 (tmm) cc_final: 0.7574 (tpp) REVERT: G 42 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8038 (pp20) REVERT: G 48 ASP cc_start: 0.6960 (t70) cc_final: 0.6748 (t0) REVERT: S 3 GLN cc_start: 0.7014 (tp40) cc_final: 0.6485 (tt0) REVERT: S 87 ARG cc_start: 0.7143 (mtp180) cc_final: 0.6915 (mtt90) REVERT: S 89 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8714 (mm-30) REVERT: S 125 ASP cc_start: 0.8072 (p0) cc_final: 0.7789 (p0) REVERT: S 141 GLU cc_start: 0.7343 (mp0) cc_final: 0.6794 (mp0) REVERT: S 180 MET cc_start: 0.8478 (ptm) cc_final: 0.7595 (ptm) REVERT: S 208 GLU cc_start: 0.8370 (pt0) cc_final: 0.7778 (pm20) REVERT: S 211 ASP cc_start: 0.8641 (t0) cc_final: 0.8156 (t0) outliers start: 4 outliers final: 0 residues processed: 291 average time/residue: 0.1078 time to fit residues: 42.5951 Evaluate side-chains 208 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 381 VAL Chi-restraints excluded: chain B residue 95 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 99 GLN R 114 ASN R 136 ASN R 180 ASN ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 HIS R 511 ASN B 91 HIS B 340 ASN S 130 GLN S 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103299 restraints weight = 16372.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102222 restraints weight = 11345.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103290 restraints weight = 7984.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104123 restraints weight = 6714.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104275 restraints weight = 6121.154| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10439 Z= 0.127 Angle : 0.645 11.760 14158 Z= 0.329 Chirality : 0.041 0.221 1572 Planarity : 0.004 0.068 1801 Dihedral : 5.672 70.133 1422 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.90 % Allowed : 12.61 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -2.34 (0.22), residues: 1283 helix: 0.49 (0.25), residues: 423 sheet: -3.03 (0.27), residues: 255 loop : -2.37 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.015 0.001 TYR R 472 PHE 0.015 0.001 PHE R 318 TRP 0.014 0.001 TRP R 163 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10427) covalent geometry : angle 0.64258 / 0.33 (14134) SS BOND : bond 0.00476 / 0.38 ( 12) SS BOND : angle 1.55187 / 1.06 ( 24) hydrogen bonds : bond 0.04370 / 2.87 ( 428) hydrogen bonds : angle 5.16798 / 3.57 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.8439 (t80) cc_final: 0.8172 (t80) REVERT: R 305 GLU cc_start: 0.6475 (tp30) cc_final: 0.6158 (tp30) REVERT: R 339 TRP cc_start: 0.9043 (m-10) cc_final: 0.8238 (m-90) REVERT: R 397 TYR cc_start: 0.8103 (p90) cc_final: 0.7752 (p90) REVERT: R 475 PHE cc_start: 0.6350 (m-80) cc_final: 0.5681 (m-10) REVERT: R 481 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7599 (tp30) REVERT: R 486 ASP cc_start: 0.8141 (m-30) cc_final: 0.7936 (m-30) REVERT: A 200 ASP cc_start: 0.7750 (p0) cc_final: 0.7458 (t0) REVERT: A 230 TYR cc_start: 0.8572 (p90) cc_final: 0.8287 (p90) REVERT: A 243 MET cc_start: 0.8002 (tpp) cc_final: 0.7731 (tpp) REVERT: A 313 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8469 (ptp90) REVERT: B 15 LYS cc_start: 0.9174 (ttmt) cc_final: 0.8930 (mtpt) REVERT: B 61 MET cc_start: 0.8004 (ptm) cc_final: 0.7712 (ttm) REVERT: B 82 TRP cc_start: 0.9203 (m100) cc_final: 0.8375 (m100) REVERT: B 95 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8670 (pp) REVERT: B 188 MET cc_start: 0.9021 (mmm) cc_final: 0.8716 (mmm) REVERT: B 228 ASP cc_start: 0.8311 (m-30) cc_final: 0.7866 (m-30) REVERT: G 18 GLN cc_start: 0.7505 (tm-30) cc_final: 0.6825 (tm-30) REVERT: S 3 GLN cc_start: 0.8160 (tp40) cc_final: 0.7772 (tt0) REVERT: S 141 GLU cc_start: 0.8170 (mp0) cc_final: 0.7608 (mp0) REVERT: S 180 MET cc_start: 0.8628 (ptm) cc_final: 0.7956 (ptm) outliers start: 32 outliers final: 11 residues processed: 264 average time/residue: 0.0949 time to fit residues: 34.8850 Evaluate side-chains 209 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 470 HIS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 110 optimal weight: 0.1980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 ASN A 256 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 = 0.3734 r_free = 0.3734 target = 0.139216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102739 restraints weight = 16725.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.102184 restraints weight = 11135.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102707 restraints weight = 10662.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105204 restraints weight = 7340.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.105456 restraints weight = 5230.335| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10439 Z= 0.187 Angle : 0.654 11.813 14158 Z= 0.331 Chirality : 0.042 0.170 1572 Planarity : 0.004 0.065 1801 Dihedral : 5.348 57.764 1421 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.72 % Allowed : 14.70 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.89 (0.23), residues: 1283 helix: 0.87 (0.25), residues: 431 sheet: -2.74 (0.29), residues: 248 loop : -2.19 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.016 0.002 TYR A 302 PHE 0.015 0.001 PHE R 318 TRP 0.021 0.002 TRP B 297 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (10427) covalent geometry : angle 0.65143 / 0.33 (14134) SS BOND : bond 0.00442 / 0.38 ( 12) SS BOND : angle 1.47619 / 1.01 ( 24) hydrogen bonds : bond 0.04234 / 2.82 ( 428) hydrogen bonds : angle 4.94721 / 3.46 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: R 158 GLU cc_start: 0.7464 (pt0) cc_final: 0.7219 (pm20) REVERT: R 237 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8223 (t80) REVERT: R 257 ARG cc_start: 0.6996 (mmm160) cc_final: 0.6786 (ptp-170) REVERT: R 339 TRP cc_start: 0.9098 (m-10) cc_final: 0.8304 (m-90) REVERT: R 397 TYR cc_start: 0.8089 (p90) cc_final: 0.7727 (p90) REVERT: R 454 ILE cc_start: 0.8388 (mt) cc_final: 0.8073 (mt) REVERT: R 475 PHE cc_start: 0.6307 (m-80) cc_final: 0.5573 (m-10) REVERT: A 242 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7801 (mmt180) REVERT: A 277 LYS cc_start: 0.8925 (tptt) cc_final: 0.8684 (tppt) REVERT: B 15 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8949 (mtpt) REVERT: B 82 TRP cc_start: 0.9281 (m100) cc_final: 0.8463 (m100) REVERT: B 95 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8819 (pp) REVERT: B 138 GLU cc_start: 0.7175 (pp20) cc_final: 0.6815 (pp20) REVERT: B 188 MET cc_start: 0.9014 (mmm) cc_final: 0.8663 (mmm) REVERT: B 339 TRP cc_start: 0.8944 (m100) cc_final: 0.8655 (m100) REVERT: S 141 GLU cc_start: 0.8215 (mp0) cc_final: 0.7727 (mp0) REVERT: S 160 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8710 (p) REVERT: S 180 MET cc_start: 0.8731 (ptm) cc_final: 0.8103 (ptm) outliers start: 41 outliers final: 23 residues processed: 236 average time/residue: 0.0953 time to fit residues: 31.7869 Evaluate side-chains 215 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 307 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 470 HIS Chi-restraints excluded: chain R residue 530 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.103564 restraints weight = 16778.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103104 restraints weight = 10812.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103643 restraints weight = 10235.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106048 restraints weight = 7065.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.106191 restraints weight = 5162.264| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10439 Z= 0.158 Angle : 0.638 11.328 14158 Z= 0.321 Chirality : 0.041 0.163 1572 Planarity : 0.004 0.060 1801 Dihedral : 5.189 55.780 1421 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.26 % Allowed : 16.15 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.69 (0.23), residues: 1283 helix: 1.00 (0.25), residues: 437 sheet: -2.54 (0.30), residues: 247 loop : -2.12 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 117 TYR 0.019 0.002 TYR A 302 PHE 0.013 0.001 PHE R 318 TRP 0.028 0.002 TRP R 119 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (10427) covalent geometry : angle 0.63676 / 0.32 (14134) SS BOND : bond 0.00363 / 0.32 ( 12) SS BOND : angle 1.16982 / 0.85 ( 24) hydrogen bonds : bond 0.03885 / 2.57 ( 428) hydrogen bonds : angle 4.76492 / 3.33 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 237 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8205 (t80) REVERT: R 246 LEU cc_start: 0.8974 (tp) cc_final: 0.8741 (mt) REVERT: R 257 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6835 (ptp-170) REVERT: R 261 ARG cc_start: 0.6915 (ptt-90) cc_final: 0.6579 (mtm-85) REVERT: R 339 TRP cc_start: 0.9042 (m-10) cc_final: 0.8247 (m-90) REVERT: R 397 TYR cc_start: 0.8042 (p90) cc_final: 0.7713 (p90) REVERT: A 242 ARG cc_start: 0.8213 (mmm-85) cc_final: 0.7867 (mmt180) REVERT: B 15 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8972 (mtpt) REVERT: B 59 TYR cc_start: 0.9235 (m-80) cc_final: 0.8780 (m-80) REVERT: B 61 MET cc_start: 0.8019 (ttm) cc_final: 0.7818 (ttm) REVERT: B 95 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8752 (pp) REVERT: B 138 GLU cc_start: 0.7415 (pp20) cc_final: 0.6948 (pp20) REVERT: B 188 MET cc_start: 0.9010 (mmm) cc_final: 0.8682 (mmm) REVERT: B 339 TRP cc_start: 0.8927 (m100) cc_final: 0.8706 (m100) REVERT: G 21 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6884 (tmm) REVERT: S 128 MET cc_start: 0.8253 (mmm) cc_final: 0.7623 (mmm) REVERT: S 141 GLU cc_start: 0.8135 (mp0) cc_final: 0.7707 (mp0) REVERT: S 180 MET cc_start: 0.8678 (ptm) cc_final: 0.7977 (ptm) REVERT: S 208 GLU cc_start: 0.8063 (pm20) cc_final: 0.6899 (pm20) outliers start: 47 outliers final: 26 residues processed: 238 average time/residue: 0.0865 time to fit residues: 29.1265 Evaluate side-chains 226 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 117 ARG Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 237 PHE Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 530 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 511 ASN A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106942 restraints weight = 16599.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106981 restraints weight = 10543.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107806 restraints weight = 10172.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108900 restraints weight = 6542.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109434 restraints weight = 5640.728| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10439 Z= 0.122 Angle : 0.612 11.399 14158 Z= 0.307 Chirality : 0.041 0.149 1572 Planarity : 0.004 0.056 1801 Dihedral : 4.922 52.546 1421 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.81 % Allowed : 16.79 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.23), residues: 1283 helix: 1.19 (0.25), residues: 443 sheet: -2.33 (0.30), residues: 246 loop : -1.97 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 117 TYR 0.018 0.001 TYR A 302 PHE 0.010 0.001 PHE S 227 TRP 0.025 0.002 TRP B 297 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (10427) covalent geometry : angle 0.60753 / 0.31 (14134) SS BOND : bond 0.00252 / 0.21 ( 12) SS BOND : angle 1.83714 / 1.29 ( 24) hydrogen bonds : bond 0.03557 / 2.36 ( 428) hydrogen bonds : angle 4.53816 / 3.17 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 246 LEU cc_start: 0.8914 (tp) cc_final: 0.8700 (mt) REVERT: R 261 ARG cc_start: 0.6726 (ptt-90) cc_final: 0.6518 (mtm-85) REVERT: R 305 GLU cc_start: 0.6543 (tp30) cc_final: 0.6080 (tp30) REVERT: R 339 TRP cc_start: 0.8986 (m-10) cc_final: 0.8197 (m-90) REVERT: R 397 TYR cc_start: 0.7992 (p90) cc_final: 0.7675 (p90) REVERT: R 475 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: A 277 LYS cc_start: 0.8913 (tptt) cc_final: 0.8647 (tppt) REVERT: B 15 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8967 (mtpt) REVERT: B 47 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9052 (p) REVERT: B 59 TYR cc_start: 0.9139 (m-80) cc_final: 0.8831 (m-80) REVERT: B 138 GLU cc_start: 0.7527 (pp20) cc_final: 0.7057 (pp20) REVERT: B 188 MET cc_start: 0.9009 (mmm) cc_final: 0.8678 (mmm) REVERT: B 338 ILE cc_start: 0.9123 (mt) cc_final: 0.8910 (mm) REVERT: B 339 TRP cc_start: 0.8917 (m100) cc_final: 0.8446 (m100) REVERT: G 21 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6800 (tmm) REVERT: S 128 MET cc_start: 0.8192 (mmm) cc_final: 0.7563 (mmm) REVERT: S 141 GLU cc_start: 0.8111 (mp0) cc_final: 0.7684 (mp0) REVERT: S 180 MET cc_start: 0.8602 (ptm) cc_final: 0.7885 (ptm) outliers start: 53 outliers final: 31 residues processed: 254 average time/residue: 0.0912 time to fit residues: 33.4031 Evaluate side-chains 235 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 117 ARG Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 GLN A 256 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106075 restraints weight = 16854.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105885 restraints weight = 10790.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106871 restraints weight = 10085.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107686 restraints weight = 6714.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108132 restraints weight = 5999.656| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10439 Z= 0.138 Angle : 0.629 12.190 14158 Z= 0.316 Chirality : 0.041 0.225 1572 Planarity : 0.004 0.101 1801 Dihedral : 4.855 49.204 1421 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.36 % Allowed : 19.06 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.23), residues: 1283 helix: 1.26 (0.25), residues: 444 sheet: -2.23 (0.30), residues: 245 loop : -1.94 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 261 TYR 0.020 0.001 TYR A 302 PHE 0.018 0.001 PHE R 237 TRP 0.036 0.002 TRP B 297 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10427) covalent geometry : angle 0.62805 / 0.32 (14134) SS BOND : bond 0.00267 / 0.22 ( 12) SS BOND : angle 0.95004 / 0.71 ( 24) hydrogen bonds : bond 0.03591 / 2.39 ( 428) hydrogen bonds : angle 4.56041 / 3.18 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 261 ARG cc_start: 0.6845 (ptt-90) cc_final: 0.6566 (mtm-85) REVERT: R 286 MET cc_start: 0.6858 (mmm) cc_final: 0.6656 (mmm) REVERT: R 339 TRP cc_start: 0.8993 (m-10) cc_final: 0.8185 (m-90) REVERT: R 397 TYR cc_start: 0.8013 (p90) cc_final: 0.7686 (p90) REVERT: R 475 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: A 197 LYS cc_start: 0.8822 (mttt) cc_final: 0.8555 (mtpp) REVERT: B 15 LYS cc_start: 0.9207 (ttmt) cc_final: 0.8991 (mtpt) REVERT: B 47 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.9114 (p) REVERT: B 59 TYR cc_start: 0.9191 (m-80) cc_final: 0.8980 (m-80) REVERT: B 82 TRP cc_start: 0.9270 (m100) cc_final: 0.8559 (m100) REVERT: B 138 GLU cc_start: 0.7632 (pp20) cc_final: 0.7169 (pp20) REVERT: B 188 MET cc_start: 0.8968 (mmm) cc_final: 0.8632 (mmm) REVERT: B 338 ILE cc_start: 0.9164 (mt) cc_final: 0.8941 (mm) REVERT: B 339 TRP cc_start: 0.8941 (m100) cc_final: 0.8467 (m100) REVERT: G 21 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6817 (tmm) REVERT: S 68 PHE cc_start: 0.8341 (m-10) cc_final: 0.7970 (m-80) REVERT: S 128 MET cc_start: 0.8310 (mmm) cc_final: 0.7681 (mmm) REVERT: S 141 GLU cc_start: 0.8136 (mp0) cc_final: 0.7699 (mp0) REVERT: S 180 MET cc_start: 0.8487 (ptm) cc_final: 0.7849 (ptm) outliers start: 48 outliers final: 38 residues processed: 242 average time/residue: 0.0855 time to fit residues: 29.4575 Evaluate side-chains 237 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain R residue 490 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.142484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104942 restraints weight = 16784.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104916 restraints weight = 10761.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105693 restraints weight = 10799.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106303 restraints weight = 7127.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109132 restraints weight = 6192.038| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10439 Z= 0.158 Angle : 0.631 11.580 14158 Z= 0.319 Chirality : 0.042 0.222 1572 Planarity : 0.004 0.101 1801 Dihedral : 4.863 47.592 1421 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.63 % Allowed : 19.24 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.25 (0.23), residues: 1283 helix: 1.34 (0.25), residues: 441 sheet: -2.15 (0.30), residues: 245 loop : -1.93 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 485 TYR 0.010 0.001 TYR S 102 PHE 0.017 0.001 PHE R 237 TRP 0.043 0.002 TRP B 297 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (10427) covalent geometry : angle 0.63009 / 0.32 (14134) SS BOND : bond 0.00307 / 0.27 ( 12) SS BOND : angle 0.95802 / 0.72 ( 24) hydrogen bonds : bond 0.03731 / 2.48 ( 428) hydrogen bonds : angle 4.55763 / 3.17 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 261 ARG cc_start: 0.6928 (ptt-90) cc_final: 0.6656 (mtm-85) REVERT: R 339 TRP cc_start: 0.9004 (m-10) cc_final: 0.8170 (m-90) REVERT: R 397 TYR cc_start: 0.7991 (p90) cc_final: 0.7636 (p90) REVERT: R 454 ILE cc_start: 0.8390 (mt) cc_final: 0.8155 (mt) REVERT: R 475 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5995 (m-80) REVERT: A 51 LYS cc_start: 0.8851 (pttp) cc_final: 0.8530 (tptt) REVERT: A 197 LYS cc_start: 0.8813 (mttt) cc_final: 0.8532 (mtpp) REVERT: A 277 LYS cc_start: 0.8863 (tptt) cc_final: 0.8590 (tppt) REVERT: A 294 ASN cc_start: 0.7661 (m110) cc_final: 0.6860 (t0) REVERT: B 15 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8993 (mtpt) REVERT: B 47 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9130 (p) REVERT: B 82 TRP cc_start: 0.9293 (m100) cc_final: 0.8548 (m100) REVERT: B 114 CYS cc_start: 0.8730 (t) cc_final: 0.8513 (t) REVERT: B 138 GLU cc_start: 0.7753 (pp20) cc_final: 0.7309 (pp20) REVERT: B 188 MET cc_start: 0.8945 (mmm) cc_final: 0.8619 (mmm) REVERT: B 338 ILE cc_start: 0.9166 (mt) cc_final: 0.8923 (mm) REVERT: B 339 TRP cc_start: 0.8928 (m100) cc_final: 0.8388 (m100) REVERT: G 21 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6773 (tmm) REVERT: S 68 PHE cc_start: 0.8298 (m-10) cc_final: 0.7981 (m-80) REVERT: S 128 MET cc_start: 0.8254 (mmm) cc_final: 0.7606 (mmm) REVERT: S 141 GLU cc_start: 0.8158 (mp0) cc_final: 0.7757 (mp0) REVERT: S 180 MET cc_start: 0.8526 (ptm) cc_final: 0.7859 (ptm) outliers start: 51 outliers final: 40 residues processed: 236 average time/residue: 0.0921 time to fit residues: 30.9855 Evaluate side-chains 240 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 117 ARG Chi-restraints excluded: chain R residue 131 MET Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain R residue 490 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 3 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 106 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.146129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109034 restraints weight = 16697.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108940 restraints weight = 10707.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109806 restraints weight = 11002.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110570 restraints weight = 6836.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112558 restraints weight = 5966.352| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10439 Z= 0.112 Angle : 0.619 11.039 14158 Z= 0.310 Chirality : 0.041 0.208 1572 Planarity : 0.004 0.090 1801 Dihedral : 4.683 46.782 1421 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.99 % Allowed : 20.33 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -1.16 (0.23), residues: 1283 helix: 1.45 (0.25), residues: 441 sheet: -2.08 (0.30), residues: 248 loop : -1.92 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 18 TYR 0.020 0.001 TYR R 472 PHE 0.014 0.001 PHE R 237 TRP 0.026 0.002 TRP B 297 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10427) covalent geometry : angle 0.61883 / 0.31 (14134) SS BOND : bond 0.00275 / 0.24 ( 12) SS BOND : angle 0.83330 / 0.63 ( 24) hydrogen bonds : bond 0.03437 / 2.28 ( 428) hydrogen bonds : angle 4.47263 / 3.12 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 261 ARG cc_start: 0.6774 (ptt-90) cc_final: 0.6539 (mtm-85) REVERT: R 339 TRP cc_start: 0.8929 (m-10) cc_final: 0.8148 (m-90) REVERT: R 366 SER cc_start: 0.8552 (m) cc_final: 0.8298 (m) REVERT: R 397 TYR cc_start: 0.7856 (p90) cc_final: 0.7596 (p90) REVERT: R 454 ILE cc_start: 0.8350 (mt) cc_final: 0.8102 (mt) REVERT: R 475 PHE cc_start: 0.6205 (OUTLIER) cc_final: 0.5858 (m-80) REVERT: A 18 MET cc_start: 0.7544 (tmm) cc_final: 0.7307 (tmm) REVERT: A 51 LYS cc_start: 0.8875 (pttp) cc_final: 0.8565 (tptt) REVERT: A 197 LYS cc_start: 0.8811 (mttt) cc_final: 0.8548 (mtpp) REVERT: A 230 TYR cc_start: 0.7081 (p90) cc_final: 0.6681 (p90) REVERT: A 277 LYS cc_start: 0.8832 (tptt) cc_final: 0.8605 (tppt) REVERT: A 294 ASN cc_start: 0.7658 (m110) cc_final: 0.6880 (t0) REVERT: B 15 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8982 (mtpt) REVERT: B 59 TYR cc_start: 0.9038 (m-80) cc_final: 0.8660 (m-80) REVERT: B 82 TRP cc_start: 0.9207 (m100) cc_final: 0.8558 (m100) REVERT: B 138 GLU cc_start: 0.7727 (pp20) cc_final: 0.7233 (pp20) REVERT: B 188 MET cc_start: 0.8968 (mmm) cc_final: 0.8670 (mmm) REVERT: B 338 ILE cc_start: 0.9120 (mt) cc_final: 0.8890 (mm) REVERT: G 21 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6747 (tmm) REVERT: S 68 PHE cc_start: 0.8286 (m-10) cc_final: 0.7971 (m-80) REVERT: S 128 MET cc_start: 0.8229 (mmm) cc_final: 0.7614 (mmm) REVERT: S 141 GLU cc_start: 0.8134 (mp0) cc_final: 0.7769 (mp0) REVERT: S 154 LEU cc_start: 0.8175 (tt) cc_final: 0.7567 (mp) REVERT: S 180 MET cc_start: 0.8417 (ptm) cc_final: 0.7770 (ptm) outliers start: 44 outliers final: 35 residues processed: 246 average time/residue: 0.0912 time to fit residues: 32.1401 Evaluate side-chains 228 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 117 ARG Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 475 PHE Chi-restraints excluded: chain R residue 490 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 6.9990 chunk 120 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 511 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105153 restraints weight = 16840.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104652 restraints weight = 11102.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105641 restraints weight = 11048.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106151 restraints weight = 7182.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109090 restraints weight = 6296.975| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10439 Z= 0.177 Angle : 0.681 13.623 14158 Z= 0.342 Chirality : 0.042 0.200 1572 Planarity : 0.005 0.097 1801 Dihedral : 4.844 46.696 1421 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.17 % Allowed : 21.05 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.23), residues: 1283 helix: 1.42 (0.25), residues: 441 sheet: -2.15 (0.30), residues: 254 loop : -1.90 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.016 0.001 TYR A 302 PHE 0.015 0.001 PHE R 237 TRP 0.049 0.002 TRP B 297 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (10427) covalent geometry : angle 0.67962 / 0.34 (14134) SS BOND : bond 0.00335 / 0.30 ( 12) SS BOND : angle 1.15986 / 0.72 ( 24) hydrogen bonds : bond 0.03792 / 2.52 ( 428) hydrogen bonds : angle 4.57690 / 3.20 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 261 ARG cc_start: 0.6924 (ptt-90) cc_final: 0.6620 (mtm-85) REVERT: R 339 TRP cc_start: 0.9011 (m-10) cc_final: 0.8433 (m-10) REVERT: R 366 SER cc_start: 0.8527 (m) cc_final: 0.8271 (m) REVERT: R 397 TYR cc_start: 0.7907 (p90) cc_final: 0.7568 (p90) REVERT: R 454 ILE cc_start: 0.8408 (mt) cc_final: 0.8148 (mt) REVERT: A 18 MET cc_start: 0.7697 (tmm) cc_final: 0.7473 (tmm) REVERT: A 197 LYS cc_start: 0.8860 (mttt) cc_final: 0.8554 (mtpp) REVERT: A 230 TYR cc_start: 0.7358 (p90) cc_final: 0.7146 (p90) REVERT: A 277 LYS cc_start: 0.8841 (tptt) cc_final: 0.8597 (tppt) REVERT: A 294 ASN cc_start: 0.7698 (m110) cc_final: 0.6913 (t0) REVERT: B 15 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8995 (mtpt) REVERT: B 36 ASN cc_start: 0.9033 (t0) cc_final: 0.8798 (t0) REVERT: B 59 TYR cc_start: 0.9339 (m-80) cc_final: 0.8874 (m-80) REVERT: B 82 TRP cc_start: 0.9255 (m100) cc_final: 0.8573 (m100) REVERT: B 138 GLU cc_start: 0.7822 (pp20) cc_final: 0.7323 (pp20) REVERT: B 188 MET cc_start: 0.8923 (mmm) cc_final: 0.8574 (mmm) REVERT: G 21 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6799 (tmm) REVERT: S 68 PHE cc_start: 0.8291 (m-10) cc_final: 0.7966 (m-80) REVERT: S 128 MET cc_start: 0.8262 (mmm) cc_final: 0.7602 (mmm) REVERT: S 141 GLU cc_start: 0.8187 (mp0) cc_final: 0.7824 (mp0) REVERT: S 180 MET cc_start: 0.8556 (ptm) cc_final: 0.7895 (ptm) outliers start: 46 outliers final: 41 residues processed: 228 average time/residue: 0.0925 time to fit residues: 30.5223 Evaluate side-chains 229 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 117 ARG Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 341 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 490 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 0.0070 chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 218 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107394 restraints weight = 16561.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107097 restraints weight = 10863.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108273 restraints weight = 9883.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108935 restraints weight = 6597.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109523 restraints weight = 5958.655| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10439 Z= 0.135 Angle : 0.682 14.920 14158 Z= 0.337 Chirality : 0.042 0.207 1572 Planarity : 0.005 0.090 1801 Dihedral : 4.712 45.874 1421 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.18 % Allowed : 22.41 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1283 helix: 1.44 (0.25), residues: 442 sheet: -2.14 (0.30), residues: 254 loop : -1.83 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.016 0.001 TYR A 302 PHE 0.013 0.001 PHE R 237 TRP 0.038 0.002 TRP B 297 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (10427) covalent geometry : angle 0.67924 / 0.34 (14134) SS BOND : bond 0.00570 / 0.52 ( 12) SS BOND : angle 1.55856 / 1.01 ( 24) hydrogen bonds : bond 0.03622 / 2.40 ( 428) hydrogen bonds : angle 4.55947 / 3.19 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 261 ARG cc_start: 0.6819 (ptt-90) cc_final: 0.6528 (mtm-85) REVERT: R 339 TRP cc_start: 0.8980 (m-10) cc_final: 0.8160 (m-90) REVERT: R 366 SER cc_start: 0.8519 (m) cc_final: 0.8255 (m) REVERT: R 397 TYR cc_start: 0.7907 (p90) cc_final: 0.7594 (p90) REVERT: R 454 ILE cc_start: 0.8404 (mt) cc_final: 0.8151 (mt) REVERT: A 197 LYS cc_start: 0.8878 (mttt) cc_final: 0.8576 (mtpp) REVERT: A 277 LYS cc_start: 0.8825 (tptt) cc_final: 0.8571 (tppt) REVERT: A 294 ASN cc_start: 0.7720 (m110) cc_final: 0.6939 (t0) REVERT: B 15 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8991 (mtpt) REVERT: B 59 TYR cc_start: 0.9106 (m-80) cc_final: 0.8891 (m-80) REVERT: B 82 TRP cc_start: 0.9215 (m100) cc_final: 0.8552 (m100) REVERT: B 138 GLU cc_start: 0.7932 (pp20) cc_final: 0.7452 (pp20) REVERT: B 188 MET cc_start: 0.8950 (mmm) cc_final: 0.8612 (mmm) REVERT: G 21 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6777 (tmm) REVERT: S 68 PHE cc_start: 0.8293 (m-10) cc_final: 0.7974 (m-80) REVERT: S 128 MET cc_start: 0.8244 (mmm) cc_final: 0.7618 (mmm) REVERT: S 141 GLU cc_start: 0.8222 (mp0) cc_final: 0.7814 (mp0) REVERT: S 180 MET cc_start: 0.8495 (ptm) cc_final: 0.7758 (ptm) outliers start: 35 outliers final: 33 residues processed: 216 average time/residue: 0.0932 time to fit residues: 28.8978 Evaluate side-chains 220 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 90 THR Chi-restraints excluded: chain R residue 117 ARG Chi-restraints excluded: chain R residue 145 THR Chi-restraints excluded: chain R residue 234 ILE Chi-restraints excluded: chain R residue 241 THR Chi-restraints excluded: chain R residue 314 CYS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain R residue 382 ASP Chi-restraints excluded: chain R residue 392 VAL Chi-restraints excluded: chain R residue 458 LEU Chi-restraints excluded: chain R residue 469 CYS Chi-restraints excluded: chain R residue 490 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.106928 restraints weight = 16670.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106754 restraints weight = 10637.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107718 restraints weight = 10070.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108583 restraints weight = 6646.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109136 restraints weight = 5864.378| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10439 Z= 0.144 Angle : 0.673 14.616 14158 Z= 0.334 Chirality : 0.042 0.195 1572 Planarity : 0.005 0.093 1801 Dihedral : 4.702 44.768 1421 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.45 % Allowed : 22.41 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1283 helix: 1.46 (0.25), residues: 443 sheet: -2.21 (0.29), residues: 256 loop : -1.81 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.023 0.001 TYR A 230 PHE 0.013 0.001 PHE R 237 TRP 0.037 0.002 TRP B 297 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (10427) covalent geometry : angle 0.67048 / 0.33 (14134) SS BOND : bond 0.00550 / 0.49 ( 12) SS BOND : angle 1.46404 / 0.95 ( 24) hydrogen bonds : bond 0.03642 / 2.43 ( 428) hydrogen bonds : angle 4.51941 / 3.16 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.10 seconds wall clock time: 30 minutes 13.54 seconds (1813.54 seconds total)