Starting phenix.real_space_refine on Sun Nov 17 07:01:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/11_2024/8t8f_41098_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/11_2024/8t8f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/11_2024/8t8f_41098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/11_2024/8t8f_41098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/11_2024/8t8f_41098_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/11_2024/8t8f_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-5513/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: 8.63, 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: 3.08 Conformation dependent library (CDL) restraints added in 1.7 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: 1.18 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: 3.63 Time building geometry restraints manager: 3.60 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: 7.090 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.880 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- 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= 0.211 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 *********************** 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 : 1.558 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: 0.2521 time to fit residues: 70.0245 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 : 1.661 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 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= 0.237 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 *********************** 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 : 1.499 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: 0.9008 (m-80) cc_final: 0.8603 (m-80) REVERT: C 43 ASN cc_start: 0.7595 (t0) cc_final: 0.7386 (t0) REVERT: C 190 SER cc_start: 0.8640 (p) cc_final: 0.7243 (p) REVERT: C 399 LYS cc_start: 0.9312 (mtmm) cc_final: 0.8945 (mttp) REVERT: C 400 LYS cc_start: 0.8965 (ptpp) cc_final: 0.8647 (pttm) REVERT: C 403 MET cc_start: 0.8716 (mtt) cc_final: 0.8042 (mmt) REVERT: D 50 PHE cc_start: 0.7607 (t80) cc_final: 0.7171 (t80) REVERT: D 52 THR cc_start: 0.7091 (m) cc_final: 0.6459 (t) REVERT: D 53 TYR cc_start: 0.8786 (m-10) cc_final: 0.8314 (m-10) REVERT: D 58 PHE cc_start: 0.9401 (m-80) cc_final: 0.9189 (m-80) REVERT: D 969 MET cc_start: 0.6941 (ppp) cc_final: 0.6563 (ppp) REVERT: E 91 MET cc_start: 0.8292 (mmp) cc_final: 0.7791 (tpt) REVERT: E 270 MET cc_start: 0.9126 (ppp) cc_final: 0.8192 (ppp) REVERT: E 273 HIS cc_start: 0.8299 (m90) cc_final: 0.8076 (m90) REVERT: E 1001 LEU cc_start: 0.8138 (tt) cc_final: 0.7685 (tt) REVERT: E 1002 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7987 (pm20) REVERT: E 1032 LEU cc_start: 0.9216 (mt) cc_final: 0.8802 (mt) REVERT: E 1046 LEU cc_start: 0.8920 (tp) cc_final: 0.8720 (tp) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2403 time to fit residues: 63.1896 Evaluate side-chains 125 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 922 HIS ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13279 Z= 0.223 Angle : 0.657 8.692 17873 Z= 0.344 Chirality : 0.043 0.149 2018 Planarity : 0.004 0.050 2276 Dihedral : 5.263 28.619 1735 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.14 % Allowed : 4.00 % Favored : 95.86 % 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: -1.15 (0.21), residues: 1583 helix: 0.25 (0.18), residues: 802 sheet: -1.07 (0.45), residues: 125 loop : -1.96 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D1071 HIS 0.009 0.002 HIS C 513 PHE 0.023 0.002 PHE C 398 TYR 0.023 0.002 TYR C 111 ARG 0.008 0.001 ARG E 980 *********************** 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 177 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 1.539 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: 0.8325 (tpt) cc_final: 0.7775 (tpt) REVERT: B 335 LEU cc_start: 0.8809 (tp) cc_final: 0.8579 (tt) REVERT: B 392 ILE cc_start: 0.8334 (mt) cc_final: 0.8049 (mt) REVERT: B 396 PHE cc_start: 0.8199 (t80) cc_final: 0.7781 (t80) REVERT: B 412 ILE cc_start: 0.9035 (mm) cc_final: 0.8776 (tt) REVERT: B 415 MET cc_start: 0.8388 (pmm) cc_final: 0.8134 (pmm) REVERT: C 32 PHE cc_start: 0.9024 (m-80) cc_final: 0.8662 (m-80) REVERT: C 190 SER cc_start: 0.8689 (p) cc_final: 0.7082 (p) REVERT: C 399 LYS cc_start: 0.9304 (mtmm) cc_final: 0.8943 (mtmt) REVERT: C 400 LYS cc_start: 0.9102 (ptpp) cc_final: 0.8874 (pttp) REVERT: C 448 PHE cc_start: 0.7202 (m-80) cc_final: 0.6954 (m-80) REVERT: D 50 PHE cc_start: 0.7835 (t80) cc_final: 0.7299 (t80) REVERT: D 52 THR cc_start: 0.7057 (m) cc_final: 0.6490 (t) REVERT: D 53 TYR cc_start: 0.8836 (m-10) cc_final: 0.8414 (m-10) REVERT: D 66 MET cc_start: 0.0226 (ptp) cc_final: -0.0402 (ptp) REVERT: D 969 MET cc_start: 0.7053 (ppp) cc_final: 0.6735 (ppp) REVERT: D 999 MET cc_start: 0.6780 (tpt) cc_final: 0.6538 (tpt) REVERT: E 270 MET cc_start: 0.9024 (ppp) cc_final: 0.8099 (ppp) REVERT: E 273 HIS cc_start: 0.8336 (m90) cc_final: 0.8060 (m90) REVERT: E 1002 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8106 (pm20) REVERT: E 1032 LEU cc_start: 0.9215 (mt) cc_final: 0.8852 (mt) outliers start: 2 outliers final: 1 residues processed: 177 average time/residue: 0.2293 time to fit residues: 61.7259 Evaluate side-chains 125 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 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** ** D 241 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 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13279 Z= 0.223 Angle : 0.640 10.573 17873 Z= 0.335 Chirality : 0.043 0.170 2018 Planarity : 0.004 0.047 2276 Dihedral : 5.222 31.392 1735 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.07 % Allowed : 4.76 % Favored : 95.17 % 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: -1.02 (0.21), residues: 1583 helix: 0.31 (0.18), residues: 807 sheet: -0.92 (0.46), residues: 123 loop : -1.87 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E1036 HIS 0.009 0.002 HIS C 513 PHE 0.028 0.002 PHE G 326 TYR 0.016 0.002 TYR D 961 ARG 0.008 0.001 ARG C 522 *********************** 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 162 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8830 (tp) cc_final: 0.8610 (tt) REVERT: B 350 ILE cc_start: 0.7445 (mt) cc_final: 0.6659 (mt) REVERT: B 392 ILE cc_start: 0.8332 (mt) cc_final: 0.8095 (mp) REVERT: B 412 ILE cc_start: 0.9005 (mm) cc_final: 0.8782 (tt) REVERT: C 189 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8851 (mp) REVERT: C 190 SER cc_start: 0.8232 (p) cc_final: 0.6303 (t) REVERT: C 361 LEU cc_start: 0.9090 (pp) cc_final: 0.8425 (pp) REVERT: C 399 LYS cc_start: 0.9282 (mtmm) cc_final: 0.8990 (mtmm) REVERT: D 50 PHE cc_start: 0.7834 (t80) cc_final: 0.7275 (t80) REVERT: D 52 THR cc_start: 0.7043 (m) cc_final: 0.6475 (t) REVERT: D 53 TYR cc_start: 0.8881 (m-10) cc_final: 0.8416 (m-10) REVERT: D 213 ASP cc_start: 0.8874 (m-30) cc_final: 0.8425 (m-30) REVERT: E 270 MET cc_start: 0.9032 (ppp) cc_final: 0.8119 (ppp) REVERT: E 273 HIS cc_start: 0.8315 (m90) cc_final: 0.8068 (m90) REVERT: E 1001 LEU cc_start: 0.8153 (tt) cc_final: 0.7747 (tt) REVERT: E 1002 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8130 (pm20) REVERT: E 1032 LEU cc_start: 0.9304 (mt) cc_final: 0.8856 (mt) REVERT: E 1053 MET cc_start: 0.6290 (tpp) cc_final: 0.5758 (tpp) REVERT: G 320 ARG cc_start: 0.9694 (mtp85) cc_final: 0.9342 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2330 time to fit residues: 57.1208 Evaluate side-chains 119 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 137 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13279 Z= 0.161 Angle : 0.593 9.663 17873 Z= 0.305 Chirality : 0.042 0.156 2018 Planarity : 0.004 0.057 2276 Dihedral : 4.931 26.618 1735 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: -0.61 (0.21), residues: 1583 helix: 0.69 (0.18), residues: 795 sheet: -0.74 (0.48), residues: 127 loop : -1.70 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E1036 HIS 0.008 0.001 HIS C 513 PHE 0.022 0.002 PHE C 398 TYR 0.015 0.001 TYR C 307 ARG 0.007 0.000 ARG E 933 *********************** 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 : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 ILE cc_start: 0.7723 (mt) cc_final: 0.6894 (mt) REVERT: C 32 PHE cc_start: 0.9012 (m-10) cc_final: 0.8684 (m-80) REVERT: C 43 ASN cc_start: 0.7440 (t0) cc_final: 0.6147 (m-40) REVERT: C 361 LEU cc_start: 0.9040 (pp) cc_final: 0.8736 (pp) REVERT: C 389 LEU cc_start: 0.8956 (mm) cc_final: 0.8681 (mm) REVERT: C 399 LYS cc_start: 0.9205 (mtmm) cc_final: 0.8848 (mtmm) REVERT: C 403 MET cc_start: 0.8144 (mtt) cc_final: 0.7836 (mtm) REVERT: C 410 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 50 PHE cc_start: 0.7772 (t80) cc_final: 0.7159 (t80) REVERT: D 52 THR cc_start: 0.7136 (m) cc_final: 0.6511 (t) REVERT: D 53 TYR cc_start: 0.8854 (m-10) cc_final: 0.8391 (m-10) REVERT: D 213 ASP cc_start: 0.8790 (m-30) cc_final: 0.8356 (m-30) REVERT: D 1018 GLN cc_start: 0.7302 (pm20) cc_final: 0.6983 (pm20) REVERT: E 270 MET cc_start: 0.9059 (ppp) cc_final: 0.8174 (ppp) REVERT: E 273 HIS cc_start: 0.8280 (m90) cc_final: 0.8067 (m90) REVERT: E 994 PHE cc_start: 0.8718 (m-10) cc_final: 0.8408 (m-10) REVERT: E 1002 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8015 (pm20) REVERT: E 1015 ASN cc_start: 0.6488 (t0) cc_final: 0.6006 (t0) REVERT: E 1032 LEU cc_start: 0.9342 (mt) cc_final: 0.8986 (mt) REVERT: E 1053 MET cc_start: 0.6481 (tpp) cc_final: 0.5919 (tpp) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2352 time to fit residues: 60.1094 Evaluate side-chains 121 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1089 ASN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13279 Z= 0.165 Angle : 0.602 9.956 17873 Z= 0.307 Chirality : 0.042 0.232 2018 Planarity : 0.004 0.044 2276 Dihedral : 4.847 26.894 1735 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.55 (0.21), residues: 1583 helix: 0.70 (0.18), residues: 804 sheet: -0.65 (0.49), residues: 127 loop : -1.66 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E1036 HIS 0.008 0.001 HIS C 513 PHE 0.020 0.002 PHE G 326 TYR 0.013 0.001 TYR C 307 ARG 0.012 0.001 ARG E 980 *********************** 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 164 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.619 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 350 ILE cc_start: 0.7447 (mt) cc_final: 0.7113 (mt) REVERT: C 32 PHE cc_start: 0.8956 (m-10) cc_final: 0.8670 (m-80) REVERT: C 43 ASN cc_start: 0.7560 (t0) cc_final: 0.6181 (m-40) REVERT: C 361 LEU cc_start: 0.9071 (pp) cc_final: 0.8443 (pp) REVERT: C 399 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8725 (mtmm) REVERT: C 403 MET cc_start: 0.8134 (mtt) cc_final: 0.6889 (tpt) REVERT: D 50 PHE cc_start: 0.7811 (t80) cc_final: 0.7220 (t80) REVERT: D 52 THR cc_start: 0.7047 (m) cc_final: 0.6458 (t) REVERT: D 53 TYR cc_start: 0.8887 (m-10) cc_final: 0.8452 (m-10) REVERT: D 213 ASP cc_start: 0.8804 (m-30) cc_final: 0.8391 (m-30) REVERT: D 1018 GLN cc_start: 0.7372 (pm20) cc_final: 0.7049 (pm20) REVERT: E 270 MET cc_start: 0.9110 (ppp) cc_final: 0.8351 (ppp) REVERT: E 994 PHE cc_start: 0.8924 (m-10) cc_final: 0.8625 (m-10) REVERT: E 1002 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8104 (pm20) REVERT: E 1015 ASN cc_start: 0.6188 (t0) cc_final: 0.5681 (t0) REVERT: E 1032 LEU cc_start: 0.9365 (mt) cc_final: 0.8977 (mt) REVERT: E 1053 MET cc_start: 0.6713 (tpp) cc_final: 0.6135 (tpp) REVERT: G 382 MET cc_start: 0.6406 (tmm) cc_final: 0.5702 (ppp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2362 time to fit residues: 58.9511 Evaluate side-chains 121 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13279 Z= 0.158 Angle : 0.597 9.400 17873 Z= 0.302 Chirality : 0.042 0.178 2018 Planarity : 0.004 0.044 2276 Dihedral : 4.753 26.478 1735 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % 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: -0.43 (0.21), residues: 1583 helix: 0.79 (0.18), residues: 797 sheet: -0.69 (0.48), residues: 127 loop : -1.54 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E1036 HIS 0.007 0.001 HIS C 513 PHE 0.019 0.001 PHE B 399 TYR 0.018 0.001 TYR C 82 ARG 0.009 0.001 ARG E 980 *********************** 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 167 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 ILE cc_start: 0.7595 (mt) cc_final: 0.7207 (mt) REVERT: C 32 PHE cc_start: 0.8933 (m-10) cc_final: 0.8683 (m-80) REVERT: C 43 ASN cc_start: 0.7432 (t0) cc_final: 0.5936 (m-40) REVERT: C 190 SER cc_start: 0.8452 (p) cc_final: 0.7193 (t) REVERT: C 233 PHE cc_start: 0.8381 (t80) cc_final: 0.8163 (t80) REVERT: C 399 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8898 (mtmm) REVERT: C 403 MET cc_start: 0.8105 (mtt) cc_final: 0.6982 (mmt) REVERT: C 410 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7840 (mt-10) REVERT: D 50 PHE cc_start: 0.7675 (t80) cc_final: 0.6666 (t80) REVERT: D 52 THR cc_start: 0.6966 (m) cc_final: 0.6503 (p) REVERT: D 53 TYR cc_start: 0.8890 (m-10) cc_final: 0.7946 (m-10) REVERT: D 213 ASP cc_start: 0.8909 (m-30) cc_final: 0.8525 (m-30) REVERT: D 1018 GLN cc_start: 0.7286 (pm20) cc_final: 0.7015 (pm20) REVERT: E 270 MET cc_start: 0.9100 (ppp) cc_final: 0.8365 (ppp) REVERT: E 273 HIS cc_start: 0.8253 (m90) cc_final: 0.8019 (m90) REVERT: E 994 PHE cc_start: 0.8809 (m-10) cc_final: 0.8325 (m-10) REVERT: E 1002 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8083 (pm20) REVERT: E 1015 ASN cc_start: 0.6068 (t0) cc_final: 0.5527 (t0) REVERT: E 1053 MET cc_start: 0.6587 (tpp) cc_final: 0.6085 (tpp) REVERT: G 382 MET cc_start: 0.6377 (tmm) cc_final: 0.6010 (tmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2326 time to fit residues: 58.9910 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 : 1.709 ------------------------------------------------------------------------------- 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: 4.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 146 optimal weight: 0.0010 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.4368 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= 0.162 Angle : 0.608 9.718 17873 Z= 0.307 Chirality : 0.042 0.172 2018 Planarity : 0.004 0.057 2276 Dihedral : 4.711 25.783 1735 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.22), residues: 1583 helix: 0.86 (0.18), residues: 801 sheet: -0.74 (0.48), residues: 127 loop : -1.51 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.032 0.002 PHE G 326 TYR 0.020 0.001 TYR C 82 ARG 0.008 0.001 ARG E 980 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.7869 (ptp) cc_final: 0.7477 (ptp) REVERT: B 350 ILE cc_start: 0.7648 (mt) cc_final: 0.6862 (mt) REVERT: C 32 PHE cc_start: 0.8901 (m-10) cc_final: 0.8672 (m-80) REVERT: C 43 ASN cc_start: 0.7442 (t0) cc_final: 0.6954 (t0) REVERT: C 190 SER cc_start: 0.8348 (p) cc_final: 0.6914 (t) REVERT: C 361 LEU cc_start: 0.9063 (pp) cc_final: 0.8455 (pp) REVERT: C 399 LYS cc_start: 0.9126 (mtmm) cc_final: 0.8791 (mtmm) REVERT: C 403 MET cc_start: 0.8123 (mtt) cc_final: 0.7041 (tpt) REVERT: D 50 PHE cc_start: 0.7736 (t80) cc_final: 0.6724 (t80) REVERT: D 52 THR cc_start: 0.6971 (m) cc_final: 0.6530 (p) REVERT: D 53 TYR cc_start: 0.8895 (m-10) cc_final: 0.8008 (m-10) REVERT: D 213 ASP cc_start: 0.8836 (m-30) cc_final: 0.8454 (m-30) REVERT: D 1018 GLN cc_start: 0.7257 (pm20) cc_final: 0.7006 (pm20) REVERT: D 1025 GLU cc_start: 0.8548 (mp0) cc_final: 0.8337 (mp0) REVERT: E 270 MET cc_start: 0.9108 (ppp) cc_final: 0.8374 (ppp) REVERT: E 273 HIS cc_start: 0.8275 (m90) cc_final: 0.8072 (m90) REVERT: E 1002 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8112 (pm20) REVERT: E 1015 ASN cc_start: 0.6156 (t0) cc_final: 0.5672 (t0) REVERT: E 1053 MET cc_start: 0.6701 (tpp) cc_final: 0.6172 (tpp) REVERT: G 339 MET cc_start: 0.4201 (tpt) cc_final: 0.3976 (tpt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2498 time to fit residues: 63.0751 Evaluate side-chains 123 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 112 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 175 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13279 Z= 0.174 Angle : 0.622 11.724 17873 Z= 0.314 Chirality : 0.042 0.186 2018 Planarity : 0.004 0.046 2276 Dihedral : 4.751 25.541 1735 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.14 % Allowed : 0.62 % 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: -0.39 (0.22), residues: 1583 helix: 0.83 (0.18), residues: 802 sheet: -0.81 (0.48), residues: 127 loop : -1.51 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.030 0.002 PHE B 399 TYR 0.024 0.002 TYR G 327 ARG 0.013 0.001 ARG E 980 *********************** 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 166 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 350 ILE cc_start: 0.7202 (mt) cc_final: 0.6760 (mt) REVERT: C 32 PHE cc_start: 0.8975 (m-10) cc_final: 0.8705 (m-80) REVERT: C 43 ASN cc_start: 0.7598 (t0) cc_final: 0.7132 (t0) REVERT: C 187 SER cc_start: 0.8882 (m) cc_final: 0.8376 (t) REVERT: C 190 SER cc_start: 0.8324 (p) cc_final: 0.6597 (t) REVERT: C 233 PHE cc_start: 0.8258 (t80) cc_final: 0.8008 (t80) REVERT: C 361 LEU cc_start: 0.9066 (pp) cc_final: 0.8526 (pp) REVERT: C 399 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8809 (mtmm) REVERT: C 403 MET cc_start: 0.8034 (mtt) cc_final: 0.7809 (mtm) REVERT: D 50 PHE cc_start: 0.7768 (t80) cc_final: 0.6731 (t80) REVERT: D 52 THR cc_start: 0.6939 (m) cc_final: 0.6548 (p) REVERT: D 53 TYR cc_start: 0.8894 (m-10) cc_final: 0.7973 (m-10) REVERT: D 213 ASP cc_start: 0.8830 (m-30) cc_final: 0.8432 (m-30) REVERT: D 1018 GLN cc_start: 0.7243 (pm20) cc_final: 0.6974 (pm20) REVERT: E 270 MET cc_start: 0.9129 (ppp) cc_final: 0.8400 (ppp) REVERT: E 1002 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8102 (pm20) REVERT: E 1015 ASN cc_start: 0.6121 (t0) cc_final: 0.5634 (t0) REVERT: E 1053 MET cc_start: 0.6908 (tpp) cc_final: 0.6369 (tpp) REVERT: G 339 MET cc_start: 0.4384 (tpt) cc_final: 0.4118 (tpt) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.2194 time to fit residues: 56.1703 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 : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13279 Z= 0.203 Angle : 0.651 9.249 17873 Z= 0.330 Chirality : 0.043 0.188 2018 Planarity : 0.004 0.049 2276 Dihedral : 4.890 26.275 1735 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.94 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: -0.53 (0.22), residues: 1583 helix: 0.67 (0.18), residues: 814 sheet: -0.68 (0.49), residues: 123 loop : -1.61 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.025 0.002 PHE B 399 TYR 0.021 0.002 TYR G 327 ARG 0.013 0.001 ARG E 980 ********************** 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 165 residues out of total 1484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 MET cc_start: 0.7581 (ptp) cc_final: 0.7074 (ptp) REVERT: B 287 MET cc_start: 0.7972 (ttm) cc_final: 0.7428 (ttt) REVERT: B 350 ILE cc_start: 0.7412 (mt) cc_final: 0.7078 (mt) REVERT: C 43 ASN cc_start: 0.7698 (t0) cc_final: 0.7267 (t0) REVERT: C 187 SER cc_start: 0.8935 (m) cc_final: 0.8470 (t) REVERT: C 189 ILE cc_start: 0.9016 (mp) cc_final: 0.8762 (mp) REVERT: C 190 SER cc_start: 0.8337 (p) cc_final: 0.6561 (t) REVERT: C 361 LEU cc_start: 0.9083 (pp) cc_final: 0.8529 (pp) REVERT: C 399 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8755 (mtmm) REVERT: C 403 MET cc_start: 0.7994 (mtt) cc_final: 0.6831 (mmt) REVERT: D 50 PHE cc_start: 0.7774 (t80) cc_final: 0.6730 (t80) REVERT: D 52 THR cc_start: 0.7077 (m) cc_final: 0.6777 (p) REVERT: D 53 TYR cc_start: 0.8927 (m-10) cc_final: 0.8062 (m-10) REVERT: D 213 ASP cc_start: 0.8811 (m-30) cc_final: 0.8378 (m-30) REVERT: D 1018 GLN cc_start: 0.7048 (pm20) cc_final: 0.6792 (pm20) REVERT: E 270 MET cc_start: 0.9122 (ppp) cc_final: 0.8465 (ppp) REVERT: E 273 HIS cc_start: 0.8410 (m90) cc_final: 0.8063 (m-70) REVERT: E 1002 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8132 (pm20) REVERT: E 1015 ASN cc_start: 0.6278 (t0) cc_final: 0.5832 (t0) REVERT: E 1053 MET cc_start: 0.7064 (tpp) cc_final: 0.6715 (tpp) REVERT: G 339 MET cc_start: 0.4680 (tpt) cc_final: 0.4424 (tpt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2297 time to fit residues: 59.2845 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 : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.4980 chunk 116 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 23 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.099702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.081204 restraints weight = 87319.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.082545 restraints weight = 65834.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.083396 restraints weight = 48653.866| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13279 Z= 0.156 Angle : 0.609 11.739 17873 Z= 0.304 Chirality : 0.042 0.174 2018 Planarity : 0.004 0.044 2276 Dihedral : 4.691 27.445 1735 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % 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: -0.39 (0.22), residues: 1583 helix: 0.86 (0.18), residues: 806 sheet: -0.77 (0.49), residues: 127 loop : -1.58 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.030 0.002 PHE E 96 TYR 0.021 0.001 TYR G 327 ARG 0.013 0.001 ARG E 980 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2552.45 seconds wall clock time: 47 minutes 58.96 seconds (2878.96 seconds total)