Starting phenix.real_space_refine on Thu May 15 12:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t8f_41098/05_2025/8t8f_41098_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t8f_41098/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t8f_41098/05_2025/8t8f_41098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t8f_41098/05_2025/8t8f_41098.map" model { file = "/net/cci-nas-00/data/ceres_data/8t8f_41098/05_2025/8t8f_41098_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t8f_41098/05_2025/8t8f_41098_neut.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'HIS: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: {'GLN:plan1': 1, 'ASP:plan': 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: {'TYR:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 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: 8.64, per 1000 atoms: 0.66 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: 3.32 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.50 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: 3.78 Time building geometry restraints manager: 3.89 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: 3.690 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.650 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.048 0.004 TRP B 200 HIS 0.015 0.001 HIS C 513 PHE 0.039 0.002 PHE B 290 TYR 0.021 0.002 TYR G 327 ARG 0.005 0.001 ARG G 361 Details of bonding type rmsd hydrogen bonds : bond 0.18718 ( 584) hydrogen bonds : angle 6.66901 ( 1680) covalent geometry : bond 0.00335 (13279) covalent geometry : angle 0.74966 (17873) *********************** 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 : 1.679 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 324 MET cc_start: 0.7925 (tpt) cc_final: 0.7673 (tpt) REVERT: B 335 LEU cc_start: 0.8795 (tp) cc_final: 0.8561 (tt) REVERT: B 393 ILE cc_start: 0.8871 (pt) cc_final: 0.8653 (mt) REVERT: C 400 LYS cc_start: 0.9076 (ptpp) cc_final: 0.8722 (pttp) REVERT: C 403 MET cc_start: 0.8817 (mtt) cc_final: 0.8405 (tpt) REVERT: C 478 ASN cc_start: 0.9265 (t0) cc_final: 0.8869 (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: 0.6746 (ppp) REVERT: D 1014 ASP cc_start: 0.6853 (m-30) cc_final: 0.5051 (m-30) REVERT: D 1020 MET cc_start: 0.5198 (ppp) cc_final: 0.4712 (ppp) REVERT: E 91 MET cc_start: 0.8135 (mmp) cc_final: 0.7443 (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: 0.8925 (m-30) REVERT: E 1002 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7931 (pm20) REVERT: E 1032 LEU cc_start: 0.9212 (mt) cc_final: 0.8970 (mt) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.2503 time to fit residues: 69.2363 Evaluate side-chains 139 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 984 HIS ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 376 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.101475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.081670 restraints weight = 85079.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.083411 restraints weight = 60040.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.084573 restraints weight = 45895.037| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13279 Z= 0.175 Angle : 0.669 10.287 17873 Z= 0.353 Chirality : 0.044 0.166 2018 Planarity : 0.004 0.053 2276 Dihedral : 5.231 29.401 1735 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.07 % Allowed : 5.18 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1583 helix: 0.26 (0.18), residues: 793 sheet: -0.88 (0.49), residues: 111 loop : -2.10 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D1071 HIS 0.011 0.002 HIS D 922 PHE 0.021 0.002 PHE B 321 TYR 0.022 0.002 TYR C 111 ARG 0.006 0.001 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 584) hydrogen bonds : angle 4.95102 ( 1680) covalent geometry : bond 0.00373 (13279) covalent geometry : angle 0.66925 (17873) *********************** 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 177 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 1.538 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: C 32 PHE cc_start: 0.9083 (m-80) cc_final: 0.8609 (m-80) REVERT: C 94 ASN cc_start: 0.7526 (t0) cc_final: 0.7246 (m-40) REVERT: C 190 SER cc_start: 0.8805 (p) cc_final: 0.7317 (p) REVERT: C 399 LYS cc_start: 0.9270 (mtmm) cc_final: 0.8894 (mttp) REVERT: C 400 LYS cc_start: 0.8956 (ptpp) cc_final: 0.8632 (pttm) REVERT: C 403 MET cc_start: 0.8676 (mtt) cc_final: 0.8038 (mmt) REVERT: D 50 PHE cc_start: 0.7725 (t80) cc_final: 0.7281 (t80) REVERT: D 52 THR cc_start: 0.7151 (m) cc_final: 0.6543 (t) REVERT: D 53 TYR cc_start: 0.8842 (m-10) cc_final: 0.8392 (m-10) REVERT: D 58 PHE cc_start: 0.9431 (m-80) cc_final: 0.9224 (m-80) REVERT: D 969 MET cc_start: 0.6988 (ppp) cc_final: 0.6603 (ppp) REVERT: E 91 MET cc_start: 0.8043 (mmp) cc_final: 0.7598 (tpt) REVERT: E 270 MET cc_start: 0.9134 (ppp) cc_final: 0.8206 (ppp) REVERT: E 273 HIS cc_start: 0.8325 (m90) cc_final: 0.8096 (m90) REVERT: E 1001 LEU cc_start: 0.8248 (tt) cc_final: 0.7777 (tt) REVERT: E 1002 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8145 (pm20) REVERT: E 1032 LEU cc_start: 0.9226 (mt) cc_final: 0.8836 (mt) REVERT: E 1046 LEU cc_start: 0.8975 (tp) cc_final: 0.8773 (tp) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2363 time to fit residues: 62.0428 Evaluate side-chains 126 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 64 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 137 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 922 HIS D1003 GLN ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.102084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.083003 restraints weight = 85422.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.084346 restraints weight = 60475.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.085059 restraints weight = 46946.771| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2221 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= 0.128 Angle : 0.610 8.786 17873 Z= 0.316 Chirality : 0.042 0.155 2018 Planarity : 0.004 0.048 2276 Dihedral : 5.088 28.784 1735 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1583 helix: 0.47 (0.18), residues: 796 sheet: -0.89 (0.49), residues: 111 loop : -1.94 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D1071 HIS 0.009 0.001 HIS C 513 PHE 0.020 0.002 PHE C 398 TYR 0.016 0.001 TYR C 111 ARG 0.007 0.001 ARG E 980 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 584) hydrogen bonds : angle 4.64645 ( 1680) covalent geometry : bond 0.00274 (13279) covalent geometry : angle 0.60998 (17873) *********************** 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 175 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.661 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: B 324 MET cc_start: 0.8116 (tpt) cc_final: 0.7652 (tpt) REVERT: B 335 LEU cc_start: 0.8698 (tp) cc_final: 0.8432 (tt) REVERT: B 392 ILE cc_start: 0.8496 (mt) cc_final: 0.8283 (mt) REVERT: C 32 PHE cc_start: 0.9134 (m-80) cc_final: 0.8659 (m-80) REVERT: C 190 SER cc_start: 0.8714 (p) cc_final: 0.6920 (p) REVERT: C 399 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8721 (mtmm) REVERT: C 400 LYS cc_start: 0.8924 (ptpp) cc_final: 0.8706 (pttp) REVERT: C 403 MET cc_start: 0.8557 (mtt) cc_final: 0.7773 (mmt) REVERT: C 448 PHE cc_start: 0.7211 (m-80) cc_final: 0.6947 (m-80) REVERT: D 50 PHE cc_start: 0.7899 (t80) cc_final: 0.7349 (t80) REVERT: D 52 THR cc_start: 0.7183 (m) cc_final: 0.6597 (t) REVERT: D 53 TYR cc_start: 0.8758 (m-10) cc_final: 0.8298 (m-10) REVERT: D 58 PHE cc_start: 0.9393 (m-80) cc_final: 0.9192 (m-80) REVERT: D 969 MET cc_start: 0.7034 (ppp) cc_final: 0.6692 (ppp) REVERT: E 270 MET cc_start: 0.9041 (ppp) cc_final: 0.8142 (ppp) REVERT: E 273 HIS cc_start: 0.8385 (m90) cc_final: 0.8112 (m90) REVERT: E 1002 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8122 (pm20) REVERT: E 1032 LEU cc_start: 0.9266 (mt) cc_final: 0.8904 (mt) REVERT: E 1046 LEU cc_start: 0.8986 (tp) cc_final: 0.8746 (tp) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2197 time to fit residues: 58.6381 Evaluate side-chains 126 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1056 HIS ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 HIS G 368 GLN ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.093340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.073383 restraints weight = 86670.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.074263 restraints weight = 65829.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.075043 restraints weight = 52826.279| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13279 Z= 0.264 Angle : 0.809 11.844 17873 Z= 0.429 Chirality : 0.048 0.258 2018 Planarity : 0.006 0.066 2276 Dihedral : 5.871 31.054 1735 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.14 % Allowed : 5.66 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.20), residues: 1583 helix: -0.26 (0.17), residues: 806 sheet: -1.19 (0.45), residues: 123 loop : -2.05 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 200 HIS 0.013 0.003 HIS B 359 PHE 0.029 0.003 PHE C 402 TYR 0.020 0.002 TYR C 82 ARG 0.017 0.001 ARG D 954 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 584) hydrogen bonds : angle 5.34204 ( 1680) covalent geometry : bond 0.00552 (13279) covalent geometry : angle 0.80857 (17873) *********************** 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 160 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 1.494 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: B 324 MET cc_start: 0.8569 (tpt) cc_final: 0.8258 (tpt) REVERT: B 415 MET cc_start: 0.8491 (pmm) cc_final: 0.8272 (pmm) REVERT: C 67 ASP cc_start: 0.8908 (p0) cc_final: 0.8701 (p0) REVERT: C 191 CYS cc_start: 0.8988 (t) cc_final: 0.8704 (t) REVERT: C 399 LYS cc_start: 0.9317 (mtmm) cc_final: 0.9066 (mttp) REVERT: D 50 PHE cc_start: 0.7994 (t80) cc_final: 0.7383 (t80) REVERT: D 52 THR cc_start: 0.7254 (m) cc_final: 0.6673 (t) REVERT: D 53 TYR cc_start: 0.8914 (m-10) cc_final: 0.8462 (m-10) REVERT: E 270 MET cc_start: 0.9021 (ppp) cc_final: 0.8113 (ppp) REVERT: E 273 HIS cc_start: 0.8448 (m90) cc_final: 0.8123 (m90) REVERT: E 1001 LEU cc_start: 0.8196 (tt) cc_final: 0.7924 (tt) REVERT: E 1002 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8519 (mp0) REVERT: E 1032 LEU cc_start: 0.9357 (mt) cc_final: 0.8799 (mt) REVERT: E 1053 MET cc_start: 0.6623 (tpp) cc_final: 0.6363 (tpp) REVERT: G 320 ARG cc_start: 0.9675 (mtp85) cc_final: 0.9431 (tpp-160) REVERT: G 323 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8276 (mp0) REVERT: G 382 MET cc_start: 0.6046 (tmm) cc_final: 0.5695 (tmm) outliers start: 2 outliers final: 0 residues processed: 160 average time/residue: 0.2413 time to fit residues: 57.8413 Evaluate side-chains 117 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 88 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 149 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 GLN 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 226 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 ASN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.096403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.077768 restraints weight = 85193.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078827 restraints weight = 64704.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.079607 restraints weight = 47421.943| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13279 Z= 0.142 Angle : 0.641 9.908 17873 Z= 0.332 Chirality : 0.043 0.171 2018 Planarity : 0.005 0.102 2276 Dihedral : 5.380 27.862 1735 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1583 helix: 0.21 (0.18), residues: 810 sheet: -0.84 (0.47), residues: 123 loop : -1.91 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E1036 HIS 0.008 0.001 HIS C 513 PHE 0.025 0.002 PHE G 326 TYR 0.019 0.002 TYR E 284 ARG 0.007 0.001 ARG C 522 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 584) hydrogen bonds : angle 4.75937 ( 1680) covalent geometry : bond 0.00310 (13279) covalent geometry : angle 0.64141 (17873) *********************** 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 169 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 PHE cc_start: 0.7321 (t80) cc_final: 0.7005 (t80) REVERT: B 415 MET cc_start: 0.8243 (pmm) cc_final: 0.7980 (pmm) REVERT: C 32 PHE cc_start: 0.9164 (m-10) cc_final: 0.8837 (m-80) REVERT: C 361 LEU cc_start: 0.9026 (pp) cc_final: 0.8393 (pp) REVERT: C 399 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8725 (mtmm) REVERT: C 403 MET cc_start: 0.8248 (mtt) cc_final: 0.7174 (tpt) REVERT: D 50 PHE cc_start: 0.7902 (t80) cc_final: 0.7256 (t80) REVERT: D 52 THR cc_start: 0.7323 (m) cc_final: 0.6679 (t) REVERT: D 53 TYR cc_start: 0.8764 (m-10) cc_final: 0.8203 (m-10) REVERT: D 213 ASP cc_start: 0.8762 (m-30) cc_final: 0.8258 (m-30) REVERT: D 1018 GLN cc_start: 0.7002 (pm20) cc_final: 0.6615 (pm20) REVERT: D 1067 MET cc_start: -0.6149 (tpp) cc_final: -0.6707 (ttt) REVERT: E 270 MET cc_start: 0.9132 (ppp) cc_final: 0.8396 (ppp) REVERT: E 273 HIS cc_start: 0.8403 (m90) cc_final: 0.8142 (m90) REVERT: E 1002 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8177 (pm20) REVERT: E 1015 ASN cc_start: 0.5711 (t0) cc_final: 0.5338 (t0) REVERT: E 1032 LEU cc_start: 0.9420 (mt) cc_final: 0.8942 (mt) REVERT: E 1053 MET cc_start: 0.6915 (tpp) cc_final: 0.6313 (tpp) REVERT: G 320 ARG cc_start: 0.9656 (mtp85) cc_final: 0.9452 (ttp-110) REVERT: G 323 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8207 (pp20) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2204 time to fit residues: 56.7310 Evaluate side-chains 120 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 155 HIS ** 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 = 0.4038 r_free = 0.4038 target = 0.092493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073043 restraints weight = 88008.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.074557 restraints weight = 64376.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.075652 restraints weight = 50596.268| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13279 Z= 0.222 Angle : 0.746 9.682 17873 Z= 0.392 Chirality : 0.046 0.166 2018 Planarity : 0.005 0.071 2276 Dihedral : 5.660 28.772 1735 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1583 helix: -0.16 (0.17), residues: 822 sheet: -1.06 (0.49), residues: 117 loop : -1.93 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP B 200 HIS 0.013 0.002 HIS B 328 PHE 0.027 0.003 PHE B 321 TYR 0.023 0.002 TYR C 111 ARG 0.009 0.001 ARG C 522 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 584) hydrogen bonds : angle 5.05918 ( 1680) covalent geometry : bond 0.00471 (13279) covalent geometry : angle 0.74642 (17873) *********************** 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 155 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 PHE cc_start: 0.8195 (t80) cc_final: 0.7866 (t80) REVERT: B 411 PHE cc_start: 0.7541 (t80) cc_final: 0.7314 (t80) REVERT: C 32 PHE cc_start: 0.8928 (m-10) cc_final: 0.8651 (m-80) REVERT: C 43 ASN cc_start: 0.8212 (t0) cc_final: 0.7912 (t0) REVERT: C 361 LEU cc_start: 0.9162 (pp) cc_final: 0.8539 (pp) REVERT: C 403 MET cc_start: 0.8464 (mtt) cc_final: 0.8250 (mtt) REVERT: D 50 PHE cc_start: 0.7918 (t80) cc_final: 0.6860 (t80) REVERT: D 52 THR cc_start: 0.7221 (m) cc_final: 0.6769 (p) REVERT: D 53 TYR cc_start: 0.8998 (m-10) cc_final: 0.8127 (m-10) REVERT: D 1018 GLN cc_start: 0.7022 (pm20) cc_final: 0.6619 (pm20) REVERT: E 270 MET cc_start: 0.9108 (ppp) cc_final: 0.8352 (ppp) REVERT: E 273 HIS cc_start: 0.8421 (m90) cc_final: 0.8122 (m90) REVERT: E 1002 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8268 (mp0) REVERT: E 1015 ASN cc_start: 0.6559 (t0) cc_final: 0.6054 (t0) REVERT: E 1032 LEU cc_start: 0.9186 (mt) cc_final: 0.8945 (mt) REVERT: E 1053 MET cc_start: 0.7167 (tpp) cc_final: 0.6638 (tpp) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2401 time to fit residues: 55.8166 Evaluate side-chains 109 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 148 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 HIS D 71 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.093990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074699 restraints weight = 87552.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.076164 restraints weight = 64040.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.077275 restraints weight = 50286.042| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13279 Z= 0.166 Angle : 0.680 8.927 17873 Z= 0.353 Chirality : 0.044 0.173 2018 Planarity : 0.005 0.063 2276 Dihedral : 5.485 26.526 1735 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 0.07 % Allowed : 1.52 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.21), residues: 1583 helix: 0.01 (0.17), residues: 823 sheet: -1.03 (0.48), residues: 121 loop : -1.87 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E1036 HIS 0.007 0.001 HIS B 201 PHE 0.029 0.002 PHE B 399 TYR 0.020 0.002 TYR C 82 ARG 0.011 0.001 ARG E 980 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 584) hydrogen bonds : angle 4.88911 ( 1680) covalent geometry : bond 0.00357 (13279) covalent geometry : angle 0.67968 (17873) *********************** 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 158 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 MET cc_start: 0.6092 (tpt) cc_final: 0.5874 (tpt) REVERT: B 324 MET cc_start: 0.8830 (tpt) cc_final: 0.8619 (tpt) REVERT: B 460 PHE cc_start: 0.8630 (m-10) cc_final: 0.8424 (m-80) REVERT: C 32 PHE cc_start: 0.8920 (m-10) cc_final: 0.8704 (m-80) REVERT: C 43 ASN cc_start: 0.8204 (t0) cc_final: 0.7906 (t0) REVERT: C 67 ASP cc_start: 0.8905 (p0) cc_final: 0.8705 (p0) REVERT: C 187 SER cc_start: 0.8786 (m) cc_final: 0.8323 (t) REVERT: C 190 SER cc_start: 0.8665 (p) cc_final: 0.7953 (t) REVERT: C 361 LEU cc_start: 0.9175 (pp) cc_final: 0.8525 (pp) REVERT: C 399 LYS cc_start: 0.9325 (pttm) cc_final: 0.9017 (pttm) REVERT: D 50 PHE cc_start: 0.7945 (t80) cc_final: 0.6834 (t80) REVERT: D 52 THR cc_start: 0.7104 (m) cc_final: 0.6723 (p) REVERT: D 53 TYR cc_start: 0.9045 (m-10) cc_final: 0.8123 (m-10) REVERT: E 270 MET cc_start: 0.9112 (ppp) cc_final: 0.8351 (ppp) REVERT: E 273 HIS cc_start: 0.8397 (m90) cc_final: 0.8146 (m90) REVERT: E 1001 LEU cc_start: 0.8159 (tt) cc_final: 0.7946 (tt) REVERT: E 1002 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8146 (mp0) REVERT: E 1015 ASN cc_start: 0.6330 (t0) cc_final: 0.5841 (t0) REVERT: E 1032 LEU cc_start: 0.9184 (mt) cc_final: 0.8886 (mt) REVERT: E 1053 MET cc_start: 0.7346 (tpp) cc_final: 0.6774 (tpp) REVERT: G 339 MET cc_start: 0.5059 (tpt) cc_final: 0.4789 (tpt) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.2221 time to fit residues: 54.0761 Evaluate side-chains 114 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 113 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- 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 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 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.095585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.076460 restraints weight = 88765.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.078046 restraints weight = 63196.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.079166 restraints weight = 48502.924| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13279 Z= 0.142 Angle : 0.657 11.902 17873 Z= 0.337 Chirality : 0.044 0.160 2018 Planarity : 0.004 0.057 2276 Dihedral : 5.304 27.542 1735 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.07 % Allowed : 1.24 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1583 helix: 0.24 (0.18), residues: 822 sheet: -1.00 (0.48), residues: 121 loop : -1.72 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E1036 HIS 0.007 0.001 HIS B 359 PHE 0.028 0.002 PHE B 253 TYR 0.016 0.001 TYR C 82 ARG 0.010 0.001 ARG E 980 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 584) hydrogen bonds : angle 4.71861 ( 1680) covalent geometry : bond 0.00307 (13279) covalent geometry : angle 0.65693 (17873) *********************** 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 157 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 ILE cc_start: 0.6291 (tt) cc_final: 0.6070 (mp) REVERT: B 324 MET cc_start: 0.8769 (tpt) cc_final: 0.8543 (tpt) REVERT: B 460 PHE cc_start: 0.8592 (m-10) cc_final: 0.8390 (m-80) REVERT: C 32 PHE cc_start: 0.8830 (m-10) cc_final: 0.8567 (m-80) REVERT: C 43 ASN cc_start: 0.8161 (t0) cc_final: 0.7715 (t0) REVERT: C 187 SER cc_start: 0.8756 (m) cc_final: 0.8212 (t) REVERT: C 190 SER cc_start: 0.8723 (p) cc_final: 0.7937 (t) REVERT: C 361 LEU cc_start: 0.9167 (pp) cc_final: 0.8590 (pp) REVERT: D 50 PHE cc_start: 0.7819 (t80) cc_final: 0.6769 (t80) REVERT: D 52 THR cc_start: 0.7120 (m) cc_final: 0.6789 (p) REVERT: D 53 TYR cc_start: 0.9075 (m-10) cc_final: 0.8222 (m-10) REVERT: D 213 ASP cc_start: 0.8805 (m-30) cc_final: 0.8294 (m-30) REVERT: E 270 MET cc_start: 0.9118 (ppp) cc_final: 0.8357 (ppp) REVERT: E 273 HIS cc_start: 0.8493 (m90) cc_final: 0.8248 (m90) REVERT: E 1002 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8244 (mp0) REVERT: E 1039 MET cc_start: 0.7123 (mpp) cc_final: 0.6829 (mpp) REVERT: E 1053 MET cc_start: 0.7250 (tpp) cc_final: 0.6732 (tpp) REVERT: G 339 MET cc_start: 0.5212 (tpt) cc_final: 0.4999 (tpt) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.2172 time to fit residues: 52.7462 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 : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 16 optimal weight: 0.2980 chunk 145 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 155 optimal weight: 0.0000 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 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** D1089 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.096836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.077611 restraints weight = 86031.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.079195 restraints weight = 63141.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080293 restraints weight = 49442.315| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5338 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= 0.117 Angle : 0.633 12.871 17873 Z= 0.319 Chirality : 0.043 0.172 2018 Planarity : 0.004 0.046 2276 Dihedral : 5.023 26.429 1735 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1583 helix: 0.56 (0.18), residues: 815 sheet: -0.97 (0.48), residues: 123 loop : -1.62 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E1036 HIS 0.007 0.001 HIS C 513 PHE 0.019 0.002 PHE G 326 TYR 0.023 0.001 TYR B 222 ARG 0.011 0.001 ARG E 980 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 584) hydrogen bonds : angle 4.51302 ( 1680) covalent geometry : bond 0.00253 (13279) covalent geometry : angle 0.63253 (17873) *********************** 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 168 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.7814 (ptp) cc_final: 0.7584 (ptp) REVERT: B 460 PHE cc_start: 0.8526 (m-10) cc_final: 0.8280 (m-80) REVERT: C 32 PHE cc_start: 0.8811 (m-10) cc_final: 0.8571 (m-80) REVERT: C 43 ASN cc_start: 0.7869 (t0) cc_final: 0.7199 (m-40) REVERT: C 361 LEU cc_start: 0.9080 (pp) cc_final: 0.8492 (pp) REVERT: D 50 PHE cc_start: 0.7803 (t80) cc_final: 0.6651 (t80) REVERT: D 52 THR cc_start: 0.6825 (m) cc_final: 0.6564 (p) REVERT: D 53 TYR cc_start: 0.9054 (m-10) cc_final: 0.8103 (m-10) REVERT: D 213 ASP cc_start: 0.8666 (m-30) cc_final: 0.8181 (m-30) REVERT: E 270 MET cc_start: 0.9107 (ppp) cc_final: 0.8367 (ppp) REVERT: E 1002 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8115 (mp0) REVERT: E 1053 MET cc_start: 0.7186 (tpp) cc_final: 0.6662 (tpp) REVERT: G 339 MET cc_start: 0.4836 (tpt) cc_final: 0.4590 (tpt) outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.2374 time to fit residues: 60.7870 Evaluate side-chains 118 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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** ** 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 = 0.4122 r_free = 0.4122 target = 0.096445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.077022 restraints weight = 85533.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078637 restraints weight = 63396.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079562 restraints weight = 49580.665| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13279 Z= 0.121 Angle : 0.627 15.177 17873 Z= 0.319 Chirality : 0.043 0.163 2018 Planarity : 0.004 0.053 2276 Dihedral : 4.941 25.884 1735 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.14 % Allowed : 0.48 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.22), residues: 1583 helix: 0.63 (0.18), residues: 810 sheet: -0.84 (0.48), residues: 123 loop : -1.54 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E1036 HIS 0.007 0.001 HIS C 513 PHE 0.018 0.001 PHE G 326 TYR 0.018 0.001 TYR B 222 ARG 0.014 0.001 ARG E 980 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 584) hydrogen bonds : angle 4.49264 ( 1680) covalent geometry : bond 0.00262 (13279) covalent geometry : angle 0.62674 (17873) ********************** 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 167 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 396 PHE cc_start: 0.8329 (t80) cc_final: 0.8128 (t80) REVERT: B 460 PHE cc_start: 0.8595 (m-10) cc_final: 0.8333 (m-80) REVERT: C 32 PHE cc_start: 0.8888 (m-10) cc_final: 0.8593 (m-80) REVERT: C 43 ASN cc_start: 0.7291 (t0) cc_final: 0.6390 (m-40) REVERT: C 361 LEU cc_start: 0.9051 (pp) cc_final: 0.8472 (pp) REVERT: C 399 LYS cc_start: 0.9191 (pttm) cc_final: 0.8815 (pttm) REVERT: C 403 MET cc_start: 0.7658 (mtt) cc_final: 0.6593 (mmt) REVERT: D 50 PHE cc_start: 0.7693 (t80) cc_final: 0.6574 (t80) REVERT: D 52 THR cc_start: 0.6835 (m) cc_final: 0.6563 (p) REVERT: D 53 TYR cc_start: 0.9016 (m-10) cc_final: 0.8022 (m-10) REVERT: D 213 ASP cc_start: 0.8772 (m-30) cc_final: 0.8339 (m-30) REVERT: E 270 MET cc_start: 0.9125 (ppp) cc_final: 0.8481 (ppp) REVERT: E 273 HIS cc_start: 0.8412 (m90) cc_final: 0.8025 (m-70) REVERT: E 1002 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8032 (pm20) REVERT: E 1053 MET cc_start: 0.7330 (tpp) cc_final: 0.6772 (tpp) REVERT: G 382 MET cc_start: 0.6953 (tmm) cc_final: 0.6732 (ppp) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.2312 time to fit residues: 57.9755 Evaluate side-chains 118 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 151 optimal weight: 6.9990 chunk 77 optimal weight: 0.0770 chunk 157 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 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 166 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 = 0.4105 r_free = 0.4105 target = 0.095509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.076658 restraints weight = 87706.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.077794 restraints weight = 65927.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.078647 restraints weight = 51128.762| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13279 Z= 0.139 Angle : 0.647 12.023 17873 Z= 0.332 Chirality : 0.043 0.154 2018 Planarity : 0.004 0.049 2276 Dihedral : 5.015 24.721 1735 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1583 helix: 0.57 (0.18), residues: 814 sheet: -0.80 (0.49), residues: 123 loop : -1.53 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 240 HIS 0.007 0.001 HIS C 513 PHE 0.041 0.002 PHE C 448 TYR 0.014 0.001 TYR C 82 ARG 0.006 0.001 ARG G 320 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 584) hydrogen bonds : angle 4.62106 ( 1680) covalent geometry : bond 0.00301 (13279) covalent geometry : angle 0.64708 (17873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4050.38 seconds wall clock time: 72 minutes 15.92 seconds (4335.92 seconds total)