Starting phenix.real_space_refine on Sat Aug 23 15:55:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t8f_41098/08_2025/8t8f_41098_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t8f_41098/08_2025/8t8f_41098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t8f_41098/08_2025/8t8f_41098_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t8f_41098/08_2025/8t8f_41098_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t8f_41098/08_2025/8t8f_41098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t8f_41098/08_2025/8t8f_41098.map" } resolution = 4.8 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= 0.015 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 63 5.16 5 C 8338 2.51 5 N 2210 2.21 5 O 2439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13050 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2086 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3957 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3324 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 404} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2729 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 348} Chain breaks: 4 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "G" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 954 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 13050 At special positions: 0 Unit cell: (101.555, 148.591, 156.074, 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 63 16.00 O 2439 8.00 N 2210 7.00 C 8338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 580.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 7 sheets defined 54.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 208 through 220 Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.656A pdb=" N ARG B 274 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 316 removed outlier: 3.571A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 316 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 3.622A pdb=" N ALA B 323 " --> pdb=" O LYS B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.614A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 365 No H-bonds generated for 'chain 'B' and resid 364 through 365' Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.864A pdb=" N LEU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 401 removed outlier: 3.568A pdb=" N ILE B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 4.525A pdb=" N TYR B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 3.832A pdb=" N ILE B 440 " --> pdb=" O CYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.629A pdb=" N LYS B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 462 " --> pdb=" O ASN B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.583A pdb=" N LEU C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ALA C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 removed outlier: 4.019A pdb=" N VAL C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.746A pdb=" N THR C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 removed outlier: 4.079A pdb=" N LEU C 87 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.578A pdb=" N ILE C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 141 removed outlier: 3.648A pdb=" N THR C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.597A pdb=" N ASN C 209 " --> pdb=" O ASN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 224 removed outlier: 3.840A pdb=" N LEU C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 235 removed outlier: 3.647A pdb=" N SER C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 261 removed outlier: 3.974A pdb=" N GLN C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 274 through 277 Processing helix chain 'C' and resid 279 through 286 Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.629A pdb=" N VAL C 301 " --> pdb=" O PHE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 357 removed outlier: 3.613A pdb=" N LYS C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 349 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 365 removed outlier: 3.988A pdb=" N ARG C 364 " --> pdb=" O LYS C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.754A pdb=" N PHE C 392 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 413 through 430 removed outlier: 5.314A pdb=" N GLU C 419 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 Processing helix chain 'C' and resid 444 through 458 removed outlier: 3.680A pdb=" N PHE C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 498 removed outlier: 3.586A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU C 486 " --> pdb=" O CYS C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 529 Processing helix chain 'C' and resid 538 through 547 removed outlier: 3.553A pdb=" N VAL C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN C 544 " --> pdb=" O PRO C 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.699A pdb=" N TYR D 92 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.783A pdb=" N PHE D 102 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.733A pdb=" N VAL D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 189 removed outlier: 4.468A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.692A pdb=" N LEU D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 246 removed outlier: 3.645A pdb=" N GLN D 241 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 946 removed outlier: 3.577A pdb=" N GLN D 892 " --> pdb=" O THR D 888 " (cutoff:3.500A) Proline residue: D 905 - end of helix Proline residue: D 927 - end of helix removed outlier: 3.851A pdb=" N ASN D 946 " --> pdb=" O ARG D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 964 Processing helix chain 'D' and resid 987 through 1003 Processing helix chain 'D' and resid 1021 through 1037 removed outlier: 3.520A pdb=" N CYS D1037 " --> pdb=" O VAL D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1082 Processing helix chain 'E' and resid 115 through 125 removed outlier: 4.145A pdb=" N LEU E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 removed outlier: 3.943A pdb=" N ASN E 134 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.617A pdb=" N ILE E 143 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 208 removed outlier: 3.711A pdb=" N ILE E 204 " --> pdb=" O LYS E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.614A pdb=" N PHE E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 247 removed outlier: 3.618A pdb=" N LYS E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER E 241 " --> pdb=" O GLN E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 287 Processing helix chain 'E' and resid 924 through 966 removed outlier: 3.903A pdb=" N ARG E 933 " --> pdb=" O PHE E 929 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS E 935 " --> pdb=" O LYS E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 971 through 981 removed outlier: 3.625A pdb=" N ALA E 975 " --> pdb=" O THR E 971 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP E 978 " --> pdb=" O ASP E 974 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE E 979 " --> pdb=" O ALA E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 1021 through 1037 removed outlier: 4.393A pdb=" N SER E1027 " --> pdb=" O GLU E1023 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR E1035 " --> pdb=" O LEU E1031 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP E1036 " --> pdb=" O LEU E1032 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS E1037 " --> pdb=" O LEU E1033 " (cutoff:3.500A) Processing helix chain 'E' and resid 1054 through 1070 removed outlier: 3.933A pdb=" N ILE E1060 " --> pdb=" O VAL E1056 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 300 removed outlier: 4.137A pdb=" N CYS G 292 " --> pdb=" O GLN G 288 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE G 293 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS G 298 " --> pdb=" O LYS G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 334 removed outlier: 3.577A pdb=" N ASN G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU G 325 " --> pdb=" O SER G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 373 Processing helix chain 'G' and resid 384 through 389 removed outlier: 3.758A pdb=" N ARG G 388 " --> pdb=" O PRO G 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.724A pdb=" N ILE D 42 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS D 117 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS D 44 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 115 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG D 46 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU D 113 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 157 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 179 through 180 removed outlier: 3.552A pdb=" N VAL D1013 " --> pdb=" O PHE D1045 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D1047 " --> pdb=" O VAL D1013 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN D 65 " --> pdb=" O TYR D1044 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU D1046 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE D 67 " --> pdb=" O LEU D1046 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N MET D 66 " --> pdb=" O HIS D1064 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 950 through 956 Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 88 removed outlier: 3.886A pdb=" N GLU E 176 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU E 189 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 989 through 992 Processing sheet with id=AA6, first strand: chain 'E' and resid 1043 through 1044 Processing sheet with id=AA7, first strand: chain 'G' and resid 305 through 306 584 hydrogen bonds defined for protein. 1680 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: 1.48 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4226 1.34 - 1.46: 2748 1.46 - 1.58: 6209 1.58 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 13279 Sorted by residual: bond pdb=" CA GLN D1015 " pdb=" C GLN D1015 " ideal model delta sigma weight residual 1.523 1.601 -0.078 1.34e-02 5.57e+03 3.40e+01 bond pdb=" C TYR C 539 " pdb=" N PRO C 540 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.19e-02 7.06e+03 4.25e+00 bond pdb=" N ASN C 530 " pdb=" CA ASN C 530 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.36e+00 bond pdb=" N GLN D1015 " pdb=" CA GLN D1015 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.29e-02 6.01e+03 2.15e+00 bond pdb=" CG LYS B 286 " pdb=" CD LYS B 286 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.87e+00 ... (remaining 13274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 17447 2.08 - 4.16: 352 4.16 - 6.24: 59 6.24 - 8.32: 14 8.32 - 10.41: 1 Bond angle restraints: 17873 Sorted by residual: angle pdb=" N GLY E 970 " pdb=" CA GLY E 970 " pdb=" C GLY E 970 " ideal model delta sigma weight residual 114.48 108.68 5.80 1.19e+00 7.06e-01 2.38e+01 angle pdb=" CA GLN D1015 " pdb=" C GLN D1015 " pdb=" O GLN D1015 " ideal model delta sigma weight residual 120.51 126.97 -6.46 1.43e+00 4.89e-01 2.04e+01 angle pdb=" N ILE C 382 " pdb=" CA ILE C 382 " pdb=" C ILE C 382 " ideal model delta sigma weight residual 111.58 106.87 4.71 1.06e+00 8.90e-01 1.98e+01 angle pdb=" N ILE D 45 " pdb=" CA ILE D 45 " pdb=" C ILE D 45 " ideal model delta sigma weight residual 107.28 114.12 -6.84 1.59e+00 3.96e-01 1.85e+01 angle pdb=" N TRP B 200 " pdb=" CA TRP B 200 " pdb=" CB TRP B 200 " ideal model delta sigma weight residual 114.17 109.43 4.74 1.14e+00 7.69e-01 1.73e+01 ... (remaining 17868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 7336 17.18 - 34.37: 655 34.37 - 51.55: 115 51.55 - 68.73: 14 68.73 - 85.92: 8 Dihedral angle restraints: 8128 sinusoidal: 3344 harmonic: 4784 Sorted by residual: dihedral pdb=" CA ILE D1072 " pdb=" C ILE D1072 " pdb=" N PRO D1073 " pdb=" CA PRO D1073 " ideal model delta harmonic sigma weight residual 180.00 152.85 27.15 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASN G 376 " pdb=" C ASN G 376 " pdb=" N HIS G 377 " pdb=" CA HIS G 377 " ideal model delta harmonic sigma weight residual -180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA MET D1067 " pdb=" C MET D1067 " pdb=" N ALA D1068 " pdb=" CA ALA D1068 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1809 0.072 - 0.145: 198 0.145 - 0.217: 9 0.217 - 0.289: 0 0.289 - 0.361: 2 Chirality restraints: 2018 Sorted by residual: chirality pdb=" CA ILE D1016 " pdb=" N ILE D1016 " pdb=" C ILE D1016 " pdb=" CB ILE D1016 " both_signs ideal model delta sigma weight residual False 2.43 2.07 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA GLN D1015 " pdb=" N GLN D1015 " pdb=" C GLN D1015 " pdb=" CB GLN D1015 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ASP D1014 " pdb=" N ASP D1014 " pdb=" C ASP D1014 " pdb=" CB ASP D1014 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2015 not shown) Planarity restraints: 2276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 200 " 0.019 2.00e-02 2.50e+03 1.81e-02 8.19e+00 pdb=" CG TRP B 200 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP B 200 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 200 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 200 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 200 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 200 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 200 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 904 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO D 905 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 905 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 905 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 290 " -0.012 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE B 290 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 290 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 290 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 290 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 290 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 290 " 0.012 2.00e-02 2.50e+03 ... (remaining 2273 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1108 2.74 - 3.28: 14247 3.28 - 3.82: 21677 3.82 - 4.36: 25566 4.36 - 4.90: 41466 Nonbonded interactions: 104064 Sorted by model distance: nonbonded pdb=" O ILE C 382 " pdb=" OG SER C 386 " model vdw 2.201 3.040 nonbonded pdb=" NH1 ARG D 939 " pdb=" O ALA D1001 " model vdw 2.204 3.120 nonbonded pdb=" NH1 ARG D1011 " pdb=" OG SER D1042 " model vdw 2.212 3.120 nonbonded pdb=" O ALA C 62 " pdb=" OH TYR C 111 " model vdw 2.217 3.040 nonbonded pdb=" NH1 ARG E 190 " pdb=" O GLY E 194 " model vdw 2.219 3.120 ... (remaining 104059 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: 3.700 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13279 Z= 0.170 Angle : 0.750 10.405 17873 Z= 0.425 Chirality : 0.045 0.361 2018 Planarity : 0.004 0.061 2276 Dihedral : 13.366 85.919 5002 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.14 % Allowed : 0.62 % Favored : 99.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.21), residues: 1583 helix: -0.04 (0.18), residues: 787 sheet: -0.91 (0.50), residues: 107 loop : -2.20 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 361 TYR 0.021 0.002 TYR G 327 PHE 0.039 0.002 PHE B 290 TRP 0.048 0.004 TRP B 200 HIS 0.015 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00335 (13279) covalent geometry : angle 0.74966 (17873) hydrogen bonds : bond 0.18718 ( 584) hydrogen bonds : angle 6.66901 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 287 MET cc_start: 0.8693 (ttt) cc_final: 0.8425 (ttt) REVERT: B 324 MET cc_start: 0.7925 (tpt) cc_final: 0.7679 (tpt) REVERT: B 335 LEU cc_start: 0.8795 (tp) cc_final: 0.8563 (tt) REVERT: B 393 ILE cc_start: 0.8871 (pt) cc_final: 0.8588 (mp) REVERT: C 400 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8710 (pttp) REVERT: C 403 MET cc_start: 0.8817 (mtt) cc_final: 0.8401 (tpt) REVERT: C 478 ASN cc_start: 0.9265 (t0) cc_final: 0.8866 (m110) REVERT: D 52 THR cc_start: 0.7289 (m) cc_final: 0.7049 (t) REVERT: D 58 PHE cc_start: 0.9492 (m-80) cc_final: 0.9229 (m-80) REVERT: D 969 MET cc_start: 0.7191 (ppp) cc_final: 0.6747 (ppp) REVERT: D 1014 ASP cc_start: 0.6853 (m-30) cc_final: 0.5053 (m-30) REVERT: D 1020 MET cc_start: 0.5198 (ppp) cc_final: 0.4710 (ppp) REVERT: E 91 MET cc_start: 0.8135 (mmp) cc_final: 0.7687 (tpt) REVERT: E 270 MET cc_start: 0.8982 (ppp) cc_final: 0.8092 (ppp) REVERT: E 976 ASP cc_start: 0.9253 (m-30) cc_final: 0.8919 (m-30) REVERT: E 1002 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7927 (pm20) REVERT: E 1032 LEU cc_start: 0.9212 (mt) cc_final: 0.8969 (mt) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.0947 time to fit residues: 26.2253 Evaluate side-chains 142 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1056 HIS ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN G 376 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.096040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.076776 restraints weight = 86835.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.077951 restraints weight = 63749.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.078730 restraints weight = 50310.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079799 restraints weight = 42972.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.079722 restraints weight = 39413.514| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13279 Z= 0.256 Angle : 0.801 11.090 17873 Z= 0.425 Chirality : 0.047 0.182 2018 Planarity : 0.005 0.056 2276 Dihedral : 5.721 29.436 1735 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.28 % Allowed : 7.11 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.20), residues: 1583 helix: -0.22 (0.17), residues: 809 sheet: -1.20 (0.44), residues: 125 loop : -2.18 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 522 TYR 0.036 0.002 TYR C 111 PHE 0.033 0.003 PHE B 321 TRP 0.027 0.003 TRP D1071 HIS 0.012 0.003 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00538 (13279) covalent geometry : angle 0.80108 (17873) hydrogen bonds : bond 0.04709 ( 584) hydrogen bonds : angle 5.31803 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8750 (tp) cc_final: 0.8493 (tt) REVERT: B 392 ILE cc_start: 0.8436 (mt) cc_final: 0.8232 (mt) REVERT: B 398 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8519 (tm-30) REVERT: C 32 PHE cc_start: 0.9135 (m-80) cc_final: 0.8715 (m-80) REVERT: C 67 ASP cc_start: 0.8903 (p0) cc_final: 0.8686 (p0) REVERT: C 98 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7418 (mm-30) REVERT: C 190 SER cc_start: 0.8882 (p) cc_final: 0.7563 (p) REVERT: C 399 LYS cc_start: 0.9311 (mtmm) cc_final: 0.8954 (mtmt) REVERT: C 400 LYS cc_start: 0.9106 (ptpp) cc_final: 0.8883 (pttm) REVERT: C 403 MET cc_start: 0.8713 (mtt) cc_final: 0.7943 (mmt) REVERT: D 50 PHE cc_start: 0.7833 (t80) cc_final: 0.7386 (t80) REVERT: D 52 THR cc_start: 0.7156 (m) cc_final: 0.6599 (t) REVERT: D 53 TYR cc_start: 0.8948 (m-10) cc_final: 0.8478 (m-10) REVERT: D 58 PHE cc_start: 0.9395 (m-80) cc_final: 0.9168 (m-80) REVERT: D 969 MET cc_start: 0.7242 (ppp) cc_final: 0.6899 (ppp) REVERT: D 999 MET cc_start: 0.7056 (tpt) cc_final: 0.6764 (tpt) REVERT: D 1020 MET cc_start: 0.5304 (ppp) cc_final: 0.5092 (ppp) REVERT: E 91 MET cc_start: 0.8294 (mmp) cc_final: 0.7808 (tpt) REVERT: E 270 MET cc_start: 0.9110 (ppp) cc_final: 0.8142 (ppp) REVERT: E 273 HIS cc_start: 0.8412 (m90) cc_final: 0.8165 (m90) REVERT: E 1032 LEU cc_start: 0.9112 (mt) cc_final: 0.8591 (mt) outliers start: 4 outliers final: 1 residues processed: 180 average time/residue: 0.0925 time to fit residues: 24.8804 Evaluate side-chains 122 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 226 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 922 HIS D1003 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.099774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.080186 restraints weight = 83988.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.081487 restraints weight = 63831.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.082135 restraints weight = 46877.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.082564 restraints weight = 40806.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.082719 restraints weight = 38974.668| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13279 Z= 0.127 Angle : 0.622 9.448 17873 Z= 0.321 Chirality : 0.043 0.169 2018 Planarity : 0.004 0.062 2276 Dihedral : 5.227 31.705 1735 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.14 % Allowed : 2.83 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.21), residues: 1583 helix: 0.27 (0.18), residues: 801 sheet: -0.85 (0.46), residues: 123 loop : -1.96 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 980 TYR 0.013 0.001 TYR C 82 PHE 0.018 0.002 PHE C 448 TRP 0.019 0.002 TRP D1071 HIS 0.009 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00278 (13279) covalent geometry : angle 0.62232 (17873) hydrogen bonds : bond 0.03828 ( 584) hydrogen bonds : angle 4.78471 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8735 (tp) cc_final: 0.8471 (tt) REVERT: C 32 PHE cc_start: 0.9092 (m-80) cc_final: 0.8602 (m-80) REVERT: C 190 SER cc_start: 0.8879 (p) cc_final: 0.7153 (p) REVERT: C 361 LEU cc_start: 0.9093 (pp) cc_final: 0.8783 (pp) REVERT: C 399 LYS cc_start: 0.9226 (mtmm) cc_final: 0.8864 (mttp) REVERT: C 403 MET cc_start: 0.8366 (mtt) cc_final: 0.7739 (mmt) REVERT: C 448 PHE cc_start: 0.7184 (m-80) cc_final: 0.6887 (m-80) REVERT: D 50 PHE cc_start: 0.7817 (t80) cc_final: 0.7211 (t80) REVERT: D 52 THR cc_start: 0.7263 (m) cc_final: 0.6655 (t) REVERT: D 53 TYR cc_start: 0.8659 (m-10) cc_final: 0.8165 (m-10) REVERT: D 1067 MET cc_start: -0.5987 (ttt) cc_final: -0.6290 (ttt) REVERT: E 270 MET cc_start: 0.9061 (ppp) cc_final: 0.8072 (ppp) REVERT: E 273 HIS cc_start: 0.8347 (m90) cc_final: 0.8062 (m90) REVERT: E 1001 LEU cc_start: 0.8312 (tt) cc_final: 0.7794 (tt) REVERT: E 1002 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8137 (mp0) REVERT: E 1032 LEU cc_start: 0.9277 (mt) cc_final: 0.8843 (mt) REVERT: G 320 ARG cc_start: 0.9699 (mtp85) cc_final: 0.9333 (tpp-160) REVERT: G 382 MET cc_start: 0.5659 (tmm) cc_final: 0.5193 (tmm) outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.0966 time to fit residues: 25.8952 Evaluate side-chains 122 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 0.3980 chunk 140 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS B 364 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.099119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.078704 restraints weight = 82864.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080618 restraints weight = 59153.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.083452 restraints weight = 41720.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.083580 restraints weight = 32305.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.083637 restraints weight = 27670.532| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13279 Z= 0.121 Angle : 0.598 10.604 17873 Z= 0.310 Chirality : 0.042 0.269 2018 Planarity : 0.004 0.055 2276 Dihedral : 5.002 28.387 1735 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.21), residues: 1583 helix: 0.50 (0.18), residues: 796 sheet: -0.69 (0.48), residues: 123 loop : -1.88 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 980 TYR 0.018 0.001 TYR C 307 PHE 0.020 0.001 PHE G 326 TRP 0.016 0.002 TRP E1036 HIS 0.008 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00259 (13279) covalent geometry : angle 0.59768 (17873) hydrogen bonds : bond 0.03583 ( 584) hydrogen bonds : angle 4.54914 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8770 (tp) cc_final: 0.8477 (tt) REVERT: B 364 GLN cc_start: 0.6609 (pt0) cc_final: 0.6028 (pp30) REVERT: B 392 ILE cc_start: 0.8407 (mt) cc_final: 0.8155 (mt) REVERT: B 433 PHE cc_start: 0.8005 (m-80) cc_final: 0.7719 (m-80) REVERT: C 32 PHE cc_start: 0.9177 (m-10) cc_final: 0.8866 (m-80) REVERT: C 190 SER cc_start: 0.8725 (p) cc_final: 0.6916 (p) REVERT: C 361 LEU cc_start: 0.9062 (pp) cc_final: 0.8760 (pp) REVERT: C 399 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8969 (mttp) REVERT: C 403 MET cc_start: 0.8243 (mtt) cc_final: 0.7636 (mmt) REVERT: C 448 PHE cc_start: 0.7047 (m-80) cc_final: 0.6677 (m-10) REVERT: D 50 PHE cc_start: 0.7861 (t80) cc_final: 0.7278 (t80) REVERT: D 52 THR cc_start: 0.7152 (m) cc_final: 0.6569 (t) REVERT: D 53 TYR cc_start: 0.8813 (m-10) cc_final: 0.8331 (m-10) REVERT: D 213 ASP cc_start: 0.8834 (m-30) cc_final: 0.8325 (m-30) REVERT: D 999 MET cc_start: 0.6739 (tpt) cc_final: 0.6495 (tpt) REVERT: D 1018 GLN cc_start: 0.6655 (pm20) cc_final: 0.6388 (pm20) REVERT: D 1020 MET cc_start: 0.5495 (ppp) cc_final: 0.5086 (ppp) REVERT: E 270 MET cc_start: 0.9036 (ppp) cc_final: 0.8165 (ppp) REVERT: E 273 HIS cc_start: 0.8273 (m90) cc_final: 0.8036 (m90) REVERT: E 977 MET cc_start: 0.7000 (tmm) cc_final: 0.6769 (tmm) REVERT: E 1001 LEU cc_start: 0.8193 (tt) cc_final: 0.7979 (tt) REVERT: E 1002 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8155 (mp0) REVERT: E 1032 LEU cc_start: 0.9298 (mt) cc_final: 0.8894 (mt) REVERT: E 1053 MET cc_start: 0.6736 (tpp) cc_final: 0.6090 (tpp) REVERT: G 382 MET cc_start: 0.6110 (tmm) cc_final: 0.5547 (tmm) outliers start: 2 outliers final: 0 residues processed: 174 average time/residue: 0.0960 time to fit residues: 25.3080 Evaluate side-chains 129 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 135 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS B 364 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.099273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.079495 restraints weight = 84746.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.081354 restraints weight = 59458.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.082670 restraints weight = 45231.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.083616 restraints weight = 36607.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.084191 restraints weight = 30972.378| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13279 Z= 0.124 Angle : 0.600 9.784 17873 Z= 0.312 Chirality : 0.042 0.178 2018 Planarity : 0.004 0.051 2276 Dihedral : 4.895 25.712 1735 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.21), residues: 1583 helix: 0.59 (0.18), residues: 800 sheet: -0.59 (0.49), residues: 123 loop : -1.79 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 320 TYR 0.017 0.001 TYR E 284 PHE 0.019 0.002 PHE B 396 TRP 0.017 0.002 TRP E1036 HIS 0.008 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00265 (13279) covalent geometry : angle 0.60020 (17873) hydrogen bonds : bond 0.03541 ( 584) hydrogen bonds : angle 4.48767 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 286 LYS cc_start: 0.8381 (tptp) cc_final: 0.8175 (tppt) REVERT: B 335 LEU cc_start: 0.8786 (tp) cc_final: 0.8582 (tt) REVERT: B 392 ILE cc_start: 0.8319 (mt) cc_final: 0.8119 (mt) REVERT: C 32 PHE cc_start: 0.9115 (m-10) cc_final: 0.8759 (m-80) REVERT: C 361 LEU cc_start: 0.9049 (pp) cc_final: 0.8753 (pp) REVERT: C 399 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8695 (mttp) REVERT: C 403 MET cc_start: 0.8165 (mtt) cc_final: 0.7849 (tpt) REVERT: D 50 PHE cc_start: 0.7803 (t80) cc_final: 0.7189 (t80) REVERT: D 52 THR cc_start: 0.7232 (m) cc_final: 0.6629 (t) REVERT: D 53 TYR cc_start: 0.8859 (m-10) cc_final: 0.8395 (m-10) REVERT: D 213 ASP cc_start: 0.8772 (m-30) cc_final: 0.8248 (m-30) REVERT: D 999 MET cc_start: 0.6688 (tpt) cc_final: 0.6225 (tpt) REVERT: D 1011 ARG cc_start: 0.4870 (mtt90) cc_final: 0.4071 (tmt-80) REVERT: D 1018 GLN cc_start: 0.6838 (pm20) cc_final: 0.6405 (pm20) REVERT: E 270 MET cc_start: 0.9027 (ppp) cc_final: 0.8150 (ppp) REVERT: E 273 HIS cc_start: 0.8198 (m90) cc_final: 0.7988 (m90) REVERT: E 1002 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8193 (mp0) REVERT: E 1032 LEU cc_start: 0.9383 (mt) cc_final: 0.8934 (mt) REVERT: E 1053 MET cc_start: 0.6817 (tpp) cc_final: 0.6171 (tpp) REVERT: G 382 MET cc_start: 0.6166 (tmm) cc_final: 0.5734 (tmm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.0923 time to fit residues: 23.8496 Evaluate side-chains 123 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.095455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.076834 restraints weight = 87921.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.078056 restraints weight = 66876.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.079534 restraints weight = 49509.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.079535 restraints weight = 44011.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.079728 restraints weight = 38441.706| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13279 Z= 0.183 Angle : 0.682 9.686 17873 Z= 0.358 Chirality : 0.044 0.171 2018 Planarity : 0.005 0.055 2276 Dihedral : 5.193 26.330 1735 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.07 % Allowed : 3.24 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.21), residues: 1583 helix: 0.21 (0.18), residues: 816 sheet: -0.77 (0.51), residues: 117 loop : -1.82 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 980 TYR 0.018 0.002 TYR E 284 PHE 0.033 0.002 PHE B 253 TRP 0.021 0.003 TRP B 200 HIS 0.008 0.002 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00390 (13279) covalent geometry : angle 0.68240 (17873) hydrogen bonds : bond 0.03881 ( 584) hydrogen bonds : angle 4.73264 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.8442 (ptp) cc_final: 0.8131 (ptp) REVERT: C 43 ASN cc_start: 0.8015 (t0) cc_final: 0.7795 (t0) REVERT: C 348 LEU cc_start: 0.6806 (mt) cc_final: 0.6209 (mt) REVERT: C 361 LEU cc_start: 0.9062 (pp) cc_final: 0.8404 (pp) REVERT: C 399 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8767 (mtmt) REVERT: C 400 LYS cc_start: 0.9178 (pttp) cc_final: 0.8550 (ptpt) REVERT: C 403 MET cc_start: 0.8138 (mtt) cc_final: 0.7618 (tpt) REVERT: D 50 PHE cc_start: 0.7806 (t80) cc_final: 0.7133 (t80) REVERT: D 52 THR cc_start: 0.7322 (m) cc_final: 0.6645 (t) REVERT: D 53 TYR cc_start: 0.8754 (m-10) cc_final: 0.8180 (m-10) REVERT: D 213 ASP cc_start: 0.8742 (m-30) cc_final: 0.8228 (m-30) REVERT: E 270 MET cc_start: 0.9085 (ppp) cc_final: 0.8273 (ppp) REVERT: E 273 HIS cc_start: 0.8294 (m90) cc_final: 0.8046 (m90) REVERT: E 1002 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8175 (mp0) REVERT: E 1015 ASN cc_start: 0.5962 (t0) cc_final: 0.5497 (t0) REVERT: E 1032 LEU cc_start: 0.9406 (mt) cc_final: 0.8859 (mt) REVERT: E 1053 MET cc_start: 0.7060 (tpp) cc_final: 0.6419 (tpp) REVERT: G 382 MET cc_start: 0.6262 (tmm) cc_final: 0.5775 (tmm) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.0931 time to fit residues: 23.6865 Evaluate side-chains 113 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 93 optimal weight: 4.9990 chunk 143 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 83 optimal weight: 0.0870 chunk 130 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 HIS D 71 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 ASN E 89 ASN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.099044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.079429 restraints weight = 84949.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.081226 restraints weight = 60208.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.082494 restraints weight = 46036.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.083496 restraints weight = 37393.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.084246 restraints weight = 31705.703| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13279 Z= 0.116 Angle : 0.619 9.125 17873 Z= 0.315 Chirality : 0.043 0.154 2018 Planarity : 0.004 0.052 2276 Dihedral : 4.915 26.353 1735 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.07 % Allowed : 1.59 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.21), residues: 1583 helix: 0.62 (0.18), residues: 794 sheet: -0.48 (0.50), residues: 123 loop : -1.67 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 980 TYR 0.012 0.001 TYR C 82 PHE 0.027 0.001 PHE B 253 TRP 0.024 0.003 TRP B 200 HIS 0.007 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00246 (13279) covalent geometry : angle 0.61935 (17873) hydrogen bonds : bond 0.03406 ( 584) hydrogen bonds : angle 4.40217 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: B 286 LYS cc_start: 0.8288 (tptp) cc_final: 0.7955 (tppt) REVERT: B 396 PHE cc_start: 0.7970 (t80) cc_final: 0.7722 (t80) REVERT: B 413 LEU cc_start: 0.8206 (mt) cc_final: 0.7914 (mm) REVERT: B 433 PHE cc_start: 0.8069 (m-80) cc_final: 0.7517 (m-80) REVERT: C 32 PHE cc_start: 0.8939 (m-10) cc_final: 0.8562 (m-80) REVERT: C 43 ASN cc_start: 0.7779 (t0) cc_final: 0.6205 (m-40) REVERT: C 361 LEU cc_start: 0.9011 (pp) cc_final: 0.8398 (pp) REVERT: D 50 PHE cc_start: 0.7790 (t80) cc_final: 0.7139 (t80) REVERT: D 52 THR cc_start: 0.6989 (m) cc_final: 0.6360 (t) REVERT: D 53 TYR cc_start: 0.8851 (m-10) cc_final: 0.8292 (m-10) REVERT: D 213 ASP cc_start: 0.8715 (m-30) cc_final: 0.8158 (m-30) REVERT: D 1011 ARG cc_start: 0.5193 (mtt90) cc_final: 0.4327 (tmt-80) REVERT: D 1018 GLN cc_start: 0.8300 (pp30) cc_final: 0.7065 (pm20) REVERT: E 270 MET cc_start: 0.9136 (ppp) cc_final: 0.8458 (ppp) REVERT: E 1002 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8159 (pm20) REVERT: E 1015 ASN cc_start: 0.6368 (t0) cc_final: 0.5803 (t0) REVERT: E 1053 MET cc_start: 0.6870 (tpp) cc_final: 0.6184 (tpp) REVERT: G 382 MET cc_start: 0.6294 (tmm) cc_final: 0.5706 (tmm) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.0993 time to fit residues: 25.3875 Evaluate side-chains 122 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 146 optimal weight: 0.0070 chunk 18 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 71 ASN D 175 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 ASN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.097385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.078882 restraints weight = 84973.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.079542 restraints weight = 64204.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.080268 restraints weight = 53541.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.081845 restraints weight = 43249.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.081779 restraints weight = 36066.526| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13279 Z= 0.140 Angle : 0.640 9.629 17873 Z= 0.330 Chirality : 0.043 0.162 2018 Planarity : 0.004 0.054 2276 Dihedral : 4.897 26.107 1735 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.14 % Allowed : 1.04 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.21), residues: 1583 helix: 0.52 (0.18), residues: 808 sheet: -0.62 (0.49), residues: 123 loop : -1.62 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 980 TYR 0.012 0.001 TYR C 82 PHE 0.026 0.002 PHE E 96 TRP 0.032 0.004 TRP B 200 HIS 0.007 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00300 (13279) covalent geometry : angle 0.64040 (17873) hydrogen bonds : bond 0.03589 ( 584) hydrogen bonds : angle 4.53323 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.574 Fit side-chains REVERT: B 433 PHE cc_start: 0.8238 (m-80) cc_final: 0.7739 (m-80) REVERT: C 32 PHE cc_start: 0.8860 (m-10) cc_final: 0.8559 (m-80) REVERT: C 43 ASN cc_start: 0.7835 (t0) cc_final: 0.6222 (m-40) REVERT: C 348 LEU cc_start: 0.6685 (mt) cc_final: 0.6470 (mp) REVERT: C 361 LEU cc_start: 0.9052 (pp) cc_final: 0.8522 (pp) REVERT: D 50 PHE cc_start: 0.7760 (t80) cc_final: 0.7052 (t80) REVERT: D 52 THR cc_start: 0.7062 (m) cc_final: 0.6608 (p) REVERT: D 53 TYR cc_start: 0.8852 (m-10) cc_final: 0.8227 (m-10) REVERT: D 213 ASP cc_start: 0.8740 (m-30) cc_final: 0.8275 (m-30) REVERT: E 270 MET cc_start: 0.9147 (ppp) cc_final: 0.8498 (ppp) REVERT: E 273 HIS cc_start: 0.8399 (m90) cc_final: 0.8054 (m-70) REVERT: E 1002 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8189 (pm20) REVERT: E 1015 ASN cc_start: 0.5745 (t0) cc_final: 0.5307 (t0) REVERT: E 1032 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mt) REVERT: E 1053 MET cc_start: 0.6922 (tpp) cc_final: 0.6295 (tpp) REVERT: G 320 ARG cc_start: 0.9335 (mmm160) cc_final: 0.8581 (tpp-160) REVERT: G 382 MET cc_start: 0.5960 (tmm) cc_final: 0.5510 (tmm) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.0959 time to fit residues: 23.9476 Evaluate side-chains 112 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 175 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.097649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.077958 restraints weight = 85410.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.079629 restraints weight = 61354.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.080852 restraints weight = 47500.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.081667 restraints weight = 38885.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.082393 restraints weight = 33436.738| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13279 Z= 0.126 Angle : 0.632 11.657 17873 Z= 0.323 Chirality : 0.043 0.177 2018 Planarity : 0.004 0.058 2276 Dihedral : 4.879 25.586 1735 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.07 % Allowed : 0.97 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.21), residues: 1583 helix: 0.63 (0.18), residues: 800 sheet: -0.56 (0.50), residues: 123 loop : -1.59 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 980 TYR 0.014 0.001 TYR B 416 PHE 0.033 0.002 PHE B 399 TRP 0.036 0.004 TRP B 200 HIS 0.007 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00276 (13279) covalent geometry : angle 0.63209 (17873) hydrogen bonds : bond 0.03475 ( 584) hydrogen bonds : angle 4.46055 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: C 32 PHE cc_start: 0.8934 (m-10) cc_final: 0.8597 (m-80) REVERT: C 43 ASN cc_start: 0.7818 (t0) cc_final: 0.6271 (m-40) REVERT: C 344 SER cc_start: 0.8556 (t) cc_final: 0.8344 (m) REVERT: C 361 LEU cc_start: 0.9050 (pp) cc_final: 0.8464 (pp) REVERT: D 50 PHE cc_start: 0.7760 (t80) cc_final: 0.7047 (t80) REVERT: D 52 THR cc_start: 0.7120 (m) cc_final: 0.6734 (p) REVERT: D 53 TYR cc_start: 0.8922 (m-10) cc_final: 0.8311 (m-10) REVERT: D 213 ASP cc_start: 0.8808 (m-30) cc_final: 0.8344 (m-30) REVERT: E 270 MET cc_start: 0.9100 (ppp) cc_final: 0.8458 (ppp) REVERT: E 273 HIS cc_start: 0.8247 (m90) cc_final: 0.8002 (m-70) REVERT: E 1002 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8182 (pm20) REVERT: E 1015 ASN cc_start: 0.5991 (t0) cc_final: 0.5571 (t0) REVERT: E 1053 MET cc_start: 0.6924 (tpp) cc_final: 0.6301 (tpp) REVERT: G 320 ARG cc_start: 0.9355 (mmm160) cc_final: 0.8603 (tpp-160) REVERT: G 339 MET cc_start: 0.4285 (tpt) cc_final: 0.4032 (tpt) REVERT: G 382 MET cc_start: 0.6672 (tmm) cc_final: 0.6418 (tmm) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1075 time to fit residues: 26.8556 Evaluate side-chains 116 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.097283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.078380 restraints weight = 86158.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.079665 restraints weight = 63591.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080582 restraints weight = 49352.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.081227 restraints weight = 40429.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.081388 restraints weight = 37313.281| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13279 Z= 0.132 Angle : 0.643 11.544 17873 Z= 0.327 Chirality : 0.043 0.186 2018 Planarity : 0.004 0.059 2276 Dihedral : 4.885 25.719 1735 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.21), residues: 1583 helix: 0.60 (0.18), residues: 807 sheet: -0.53 (0.50), residues: 123 loop : -1.64 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 980 TYR 0.014 0.001 TYR C 82 PHE 0.035 0.002 PHE B 253 TRP 0.039 0.003 TRP B 200 HIS 0.007 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00287 (13279) covalent geometry : angle 0.64259 (17873) hydrogen bonds : bond 0.03478 ( 584) hydrogen bonds : angle 4.48843 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 213 MET cc_start: 0.8055 (ptp) cc_final: 0.7779 (ptp) REVERT: B 350 ILE cc_start: 0.7096 (mt) cc_final: 0.6683 (mt) REVERT: C 32 PHE cc_start: 0.8957 (m-10) cc_final: 0.8646 (m-80) REVERT: C 43 ASN cc_start: 0.7828 (t0) cc_final: 0.6327 (m-40) REVERT: C 189 ILE cc_start: 0.9249 (mp) cc_final: 0.8930 (mp) REVERT: C 191 CYS cc_start: 0.8623 (t) cc_final: 0.8329 (t) REVERT: C 233 PHE cc_start: 0.8317 (t80) cc_final: 0.8082 (t80) REVERT: C 361 LEU cc_start: 0.9067 (pp) cc_final: 0.8517 (pp) REVERT: D 50 PHE cc_start: 0.7687 (t80) cc_final: 0.6942 (t80) REVERT: D 52 THR cc_start: 0.7151 (m) cc_final: 0.6816 (p) REVERT: D 53 TYR cc_start: 0.8909 (m-10) cc_final: 0.8397 (m-10) REVERT: D 213 ASP cc_start: 0.8840 (m-30) cc_final: 0.8424 (m-30) REVERT: E 270 MET cc_start: 0.9107 (ppp) cc_final: 0.8446 (ppp) REVERT: E 273 HIS cc_start: 0.8364 (m90) cc_final: 0.8127 (m-70) REVERT: E 1002 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8210 (pm20) REVERT: E 1015 ASN cc_start: 0.5715 (t0) cc_final: 0.5436 (t0) REVERT: E 1053 MET cc_start: 0.6973 (tpp) cc_final: 0.6443 (tpp) REVERT: G 320 ARG cc_start: 0.9366 (mmm160) cc_final: 0.8592 (tpp-160) REVERT: G 339 MET cc_start: 0.4667 (tpt) cc_final: 0.4385 (tpt) REVERT: G 369 ARG cc_start: 0.6490 (mmm160) cc_final: 0.5794 (mtt180) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1054 time to fit residues: 25.9710 Evaluate side-chains 115 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 58 optimal weight: 0.0870 chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.098139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.078893 restraints weight = 86384.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080534 restraints weight = 62484.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081714 restraints weight = 48430.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.082582 restraints weight = 39788.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.083236 restraints weight = 34004.194| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13279 Z= 0.117 Angle : 0.625 11.485 17873 Z= 0.314 Chirality : 0.043 0.173 2018 Planarity : 0.004 0.057 2276 Dihedral : 4.782 27.068 1735 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.21), residues: 1583 helix: 0.74 (0.18), residues: 808 sheet: -0.42 (0.50), residues: 123 loop : -1.61 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 980 TYR 0.013 0.001 TYR C 82 PHE 0.028 0.002 PHE B 399 TRP 0.031 0.003 TRP B 200 HIS 0.007 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00255 (13279) covalent geometry : angle 0.62462 (17873) hydrogen bonds : bond 0.03363 ( 584) hydrogen bonds : angle 4.36358 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2073.39 seconds wall clock time: 36 minutes 48.99 seconds (2208.99 seconds total)