Starting phenix.real_space_refine on Sun Jul 21 03:34:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/07_2024/8t8f_41098_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/07_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_41098/07_2024/8t8f_41098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/07_2024/8t8f_41098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/07_2024/8t8f_41098_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/07_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 Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 474": "OE1" <-> "OE2" Residue "C GLU 480": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.94, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 5.07 Conformation dependent library (CDL) restraints added in 2.3 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: 1.43 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: 3.30 Time building geometry restraints manager: 5.56 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: 97.52 - 104.83: 166 104.83 - 112.14: 6415 112.14 - 119.46: 4738 119.46 - 126.77: 6449 126.77 - 134.09: 105 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 2.440 nonbonded pdb=" NH1 ARG D 939 " pdb=" O ALA D1001 " model vdw 2.204 2.520 nonbonded pdb=" NH1 ARG D1011 " pdb=" OG SER D1042 " model vdw 2.212 2.520 nonbonded pdb=" O ALA C 62 " pdb=" OH TYR C 111 " model vdw 2.217 2.440 nonbonded pdb=" NH1 ARG E 190 " pdb=" O GLY E 194 " model vdw 2.219 2.520 ... (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 ========== 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: 4.330 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: 0.090 Set scattering table: 0.130 Process input model: 36.350 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.150 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.540 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: 0.2470 time to fit residues: 68.2416 Evaluate side-chains 139 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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: 5.9990 chunk 120 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 64 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 0.3980 chunk 92 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 922 HIS D 984 HIS ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 ASN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** E 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1028 GLN G 376 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.1229 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= 0.161 Angle : 0.593 9.705 17873 Z= 0.308 Chirality : 0.041 0.182 2018 Planarity : 0.004 0.052 2276 Dihedral : 5.087 32.680 1735 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.07 % Allowed : 4.35 % Favored : 95.58 % 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: -1.04 (0.21), residues: 1583 helix: 0.43 (0.19), residues: 798 sheet: -0.49 (0.50), residues: 109 loop : -2.14 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D1071 HIS 0.011 0.001 HIS C 513 PHE 0.016 0.002 PHE B 311 TYR 0.014 0.001 TYR C 82 ARG 0.005 0.000 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 182 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.544 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: C 32 PHE cc_start: 0.9101 (m-80) cc_final: 0.8648 (m-80) REVERT: C 43 ASN cc_start: 0.7513 (t0) cc_final: 0.7212 (t0) REVERT: C 94 ASN cc_start: 0.7359 (t0) cc_final: 0.7148 (m-40) REVERT: C 190 SER cc_start: 0.8341 (p) cc_final: 0.7368 (p) REVERT: C 193 GLU cc_start: 0.8651 (pt0) cc_final: 0.8304 (pm20) REVERT: C 399 LYS cc_start: 0.9267 (mtmm) cc_final: 0.8965 (mttp) REVERT: C 400 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8556 (pttp) REVERT: C 403 MET cc_start: 0.8675 (mtt) cc_final: 0.7968 (mmt) REVERT: D 52 THR cc_start: 0.6909 (m) cc_final: 0.6656 (t) REVERT: D 969 MET cc_start: 0.6793 (ppp) cc_final: 0.6474 (ppp) REVERT: D 999 MET cc_start: 0.6567 (tpt) cc_final: 0.6128 (tpt) REVERT: D 1011 ARG cc_start: 0.4960 (mtt90) cc_final: 0.3690 (tmt-80) REVERT: E 91 MET cc_start: 0.8139 (mmp) cc_final: 0.7635 (tpt) REVERT: E 270 MET cc_start: 0.9005 (ppp) cc_final: 0.8079 (ppp) REVERT: E 273 HIS cc_start: 0.8240 (m90) cc_final: 0.7998 (m90) REVERT: E 1001 LEU cc_start: 0.8069 (tt) cc_final: 0.7587 (tt) REVERT: E 1002 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7849 (pm20) REVERT: E 1032 LEU cc_start: 0.9179 (mt) cc_final: 0.8876 (mt) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2500 time to fit residues: 66.3493 Evaluate side-chains 136 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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: 5.9990 chunk 44 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13279 Z= 0.252 Angle : 0.680 8.609 17873 Z= 0.357 Chirality : 0.044 0.278 2018 Planarity : 0.004 0.046 2276 Dihedral : 5.291 32.592 1735 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.21 % Allowed : 4.90 % Favored : 94.89 % 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: -1.08 (0.21), residues: 1583 helix: 0.33 (0.18), residues: 814 sheet: -0.83 (0.43), residues: 133 loop : -2.08 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 200 HIS 0.010 0.002 HIS C 513 PHE 0.024 0.002 PHE E 230 TYR 0.019 0.002 TYR C 111 ARG 0.013 0.001 ARG D 139 *********************** 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 fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 PHE cc_start: 0.5845 (m-10) cc_final: 0.5499 (m-10) REVERT: B 287 MET cc_start: 0.8474 (tpt) cc_final: 0.7835 (tpt) REVERT: B 335 LEU cc_start: 0.8706 (tp) cc_final: 0.8465 (tt) REVERT: B 396 PHE cc_start: 0.8286 (t80) cc_final: 0.7852 (t80) REVERT: B 412 ILE cc_start: 0.9176 (mm) cc_final: 0.8802 (tt) REVERT: C 43 ASN cc_start: 0.7816 (t0) cc_final: 0.7514 (t0) REVERT: C 190 SER cc_start: 0.8530 (p) cc_final: 0.7058 (t) REVERT: C 399 LYS cc_start: 0.9259 (mtmm) cc_final: 0.8810 (mtmm) REVERT: C 403 MET cc_start: 0.8674 (mtt) cc_final: 0.7809 (mmt) REVERT: D 52 THR cc_start: 0.7050 (m) cc_final: 0.6730 (t) REVERT: D 58 PHE cc_start: 0.9313 (m-10) cc_final: 0.9049 (m-80) REVERT: D 969 MET cc_start: 0.7034 (ppp) cc_final: 0.6721 (ppp) REVERT: D 1020 MET cc_start: 0.5533 (ppp) cc_final: 0.5239 (ppp) REVERT: E 254 GLU cc_start: 0.8823 (pt0) cc_final: 0.8580 (pp20) REVERT: E 270 MET cc_start: 0.8986 (ppp) cc_final: 0.8098 (ppp) REVERT: E 273 HIS cc_start: 0.8235 (m90) cc_final: 0.7946 (m90) REVERT: E 1001 LEU cc_start: 0.8181 (tt) cc_final: 0.7767 (tt) REVERT: E 1002 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8130 (pm20) REVERT: E 1032 LEU cc_start: 0.9300 (mt) cc_final: 0.8897 (mt) outliers start: 3 outliers final: 0 residues processed: 173 average time/residue: 0.2416 time to fit residues: 61.8339 Evaluate side-chains 119 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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: 0.9990 chunk 108 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 0.0980 chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 HIS ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.2737 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= 0.174 Angle : 0.598 10.460 17873 Z= 0.307 Chirality : 0.042 0.164 2018 Planarity : 0.003 0.045 2276 Dihedral : 5.081 29.601 1735 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % 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: -0.81 (0.21), residues: 1583 helix: 0.54 (0.18), residues: 813 sheet: -0.70 (0.49), residues: 113 loop : -1.90 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E1036 HIS 0.009 0.001 HIS C 513 PHE 0.018 0.002 PHE C 398 TYR 0.012 0.001 TYR D1044 ARG 0.005 0.000 ARG E 980 *********************** 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 174 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.8134 (tpt) cc_final: 0.7753 (tpt) REVERT: B 335 LEU cc_start: 0.8844 (tp) cc_final: 0.8515 (tt) REVERT: B 412 ILE cc_start: 0.9069 (mm) cc_final: 0.8751 (tt) REVERT: C 32 PHE cc_start: 0.9069 (m-10) cc_final: 0.8788 (m-80) REVERT: C 43 ASN cc_start: 0.7688 (t0) cc_final: 0.7408 (t0) REVERT: C 190 SER cc_start: 0.8389 (p) cc_final: 0.6439 (p) REVERT: C 361 LEU cc_start: 0.9019 (pp) cc_final: 0.8722 (pp) REVERT: C 399 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8809 (mtmm) REVERT: C 403 MET cc_start: 0.8523 (mtt) cc_final: 0.7615 (mmt) REVERT: D 50 PHE cc_start: 0.7876 (t80) cc_final: 0.7603 (t80) REVERT: D 52 THR cc_start: 0.7039 (m) cc_final: 0.6497 (t) REVERT: D 53 TYR cc_start: 0.8475 (m-10) cc_final: 0.8208 (m-10) REVERT: D 58 PHE cc_start: 0.9296 (m-10) cc_final: 0.9061 (m-80) REVERT: D 999 MET cc_start: 0.6897 (tpt) cc_final: 0.6633 (tpt) REVERT: E 270 MET cc_start: 0.8979 (ppp) cc_final: 0.8112 (ppp) REVERT: E 273 HIS cc_start: 0.8201 (m90) cc_final: 0.7916 (m90) REVERT: E 1001 LEU cc_start: 0.8161 (tt) cc_final: 0.7739 (tt) REVERT: E 1002 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8104 (pm20) REVERT: E 1032 LEU cc_start: 0.9385 (mt) cc_final: 0.9022 (mt) REVERT: G 382 MET cc_start: 0.5179 (tmm) cc_final: 0.4928 (tmm) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2427 time to fit residues: 62.9149 Evaluate side-chains 123 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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: 0.0670 chunk 2 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 51 optimal weight: 0.0870 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13279 Z= 0.144 Angle : 0.579 10.793 17873 Z= 0.296 Chirality : 0.041 0.147 2018 Planarity : 0.003 0.055 2276 Dihedral : 4.828 27.341 1735 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: 0.72 (0.19), residues: 804 sheet: -0.37 (0.51), residues: 111 loop : -1.84 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 200 HIS 0.008 0.001 HIS C 513 PHE 0.021 0.002 PHE G 326 TYR 0.019 0.001 TYR C 307 ARG 0.005 0.000 ARG G 369 *********************** 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 178 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.8173 (tpt) cc_final: 0.7777 (tpt) REVERT: B 335 LEU cc_start: 0.8737 (tp) cc_final: 0.8468 (tt) REVERT: C 32 PHE cc_start: 0.9007 (m-10) cc_final: 0.8725 (m-80) REVERT: C 36 ASN cc_start: 0.9102 (t0) cc_final: 0.8697 (t0) REVERT: C 43 ASN cc_start: 0.7463 (t0) cc_final: 0.7113 (t0) REVERT: C 361 LEU cc_start: 0.9031 (pp) cc_final: 0.8755 (pp) REVERT: C 399 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8833 (mtmm) REVERT: C 403 MET cc_start: 0.8242 (mtt) cc_final: 0.7377 (mmt) REVERT: D 50 PHE cc_start: 0.7868 (t80) cc_final: 0.7597 (t80) REVERT: D 52 THR cc_start: 0.6998 (m) cc_final: 0.6479 (t) REVERT: D 53 TYR cc_start: 0.8455 (m-10) cc_final: 0.8170 (m-10) REVERT: D 58 PHE cc_start: 0.9253 (m-10) cc_final: 0.8978 (m-80) REVERT: D 213 ASP cc_start: 0.8877 (m-30) cc_final: 0.8461 (m-30) REVERT: D 969 MET cc_start: 0.7279 (ppp) cc_final: 0.7060 (ppp) REVERT: D 1018 GLN cc_start: 0.7113 (pm20) cc_final: 0.6871 (pm20) REVERT: E 270 MET cc_start: 0.8962 (ppp) cc_final: 0.8103 (ppp) REVERT: E 273 HIS cc_start: 0.8175 (m90) cc_final: 0.7925 (m90) REVERT: E 994 PHE cc_start: 0.8695 (m-10) cc_final: 0.8379 (m-10) REVERT: E 1002 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7937 (pm20) REVERT: E 1032 LEU cc_start: 0.9381 (mt) cc_final: 0.9050 (mt) REVERT: G 320 ARG cc_start: 0.9712 (mtp85) cc_final: 0.9342 (tpp-160) REVERT: G 382 MET cc_start: 0.5473 (tmm) cc_final: 0.4930 (tmm) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2358 time to fit residues: 62.4874 Evaluate side-chains 135 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.518 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 0.4980 chunk 80 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 71 ASN D 226 GLN ** 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** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 HIS G 375 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 13279 Z= 0.470 Angle : 1.002 15.043 17873 Z= 0.532 Chirality : 0.052 0.224 2018 Planarity : 0.008 0.087 2276 Dihedral : 6.613 34.999 1735 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 37.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.49 % Favored : 89.45 % Rotamer: Outliers : 0.14 % Allowed : 4.76 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.16 (0.20), residues: 1583 helix: -0.90 (0.16), residues: 812 sheet: -0.82 (0.50), residues: 119 loop : -2.15 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP B 200 HIS 0.015 0.003 HIS B 359 PHE 0.041 0.004 PHE C 214 TYR 0.046 0.003 TYR C 111 ARG 0.025 0.002 ARG E 933 *********************** 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 149 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.8674 (tpt) cc_final: 0.8392 (tpt) REVERT: B 335 LEU cc_start: 0.9029 (tp) cc_final: 0.8815 (tt) REVERT: B 433 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: C 43 ASN cc_start: 0.8052 (t0) cc_final: 0.7660 (t0) REVERT: C 187 SER cc_start: 0.8876 (m) cc_final: 0.8364 (t) REVERT: C 189 ILE cc_start: 0.9579 (mm) cc_final: 0.9280 (mp) REVERT: C 399 LYS cc_start: 0.9274 (mtmm) cc_final: 0.9045 (mtmt) REVERT: D 50 PHE cc_start: 0.8026 (t80) cc_final: 0.7151 (t80) REVERT: D 52 THR cc_start: 0.7170 (m) cc_final: 0.6843 (p) REVERT: D 53 TYR cc_start: 0.8762 (m-10) cc_final: 0.8121 (m-10) REVERT: D 58 PHE cc_start: 0.9159 (m-10) cc_final: 0.8911 (m-80) REVERT: E 270 MET cc_start: 0.9047 (ppp) cc_final: 0.8250 (ppp) REVERT: E 273 HIS cc_start: 0.8408 (m90) cc_final: 0.8138 (m90) REVERT: E 1002 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8146 (mp0) REVERT: E 1015 ASN cc_start: 0.7260 (m-40) cc_final: 0.7038 (t0) REVERT: E 1032 LEU cc_start: 0.9287 (mt) cc_final: 0.8660 (mt) REVERT: G 320 ARG cc_start: 0.9652 (mtp85) cc_final: 0.9429 (tpp-160) REVERT: G 323 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8057 (mt-10) REVERT: G 382 MET cc_start: 0.6933 (tmm) cc_final: 0.6711 (tmm) outliers start: 2 outliers final: 0 residues processed: 149 average time/residue: 0.2351 time to fit residues: 52.6166 Evaluate side-chains 108 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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: 0.8980 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 153 optimal weight: 0.0470 chunk 95 optimal weight: 0.0030 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 HIS D 71 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13279 Z= 0.177 Angle : 0.663 10.540 17873 Z= 0.337 Chirality : 0.044 0.215 2018 Planarity : 0.004 0.050 2276 Dihedral : 5.501 25.980 1735 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.07 % Allowed : 1.66 % Favored : 98.27 % 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: -1.32 (0.21), residues: 1583 helix: -0.06 (0.17), residues: 820 sheet: -0.52 (0.52), residues: 119 loop : -1.99 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E1036 HIS 0.007 0.001 HIS C 513 PHE 0.030 0.002 PHE G 326 TYR 0.016 0.002 TYR E 284 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 169 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.8615 (tpt) cc_final: 0.8322 (tpt) REVERT: B 335 LEU cc_start: 0.8933 (tp) cc_final: 0.8710 (tt) REVERT: B 460 PHE cc_start: 0.8486 (m-10) cc_final: 0.8246 (m-80) REVERT: C 32 PHE cc_start: 0.8996 (m-80) cc_final: 0.8715 (m-80) REVERT: C 43 ASN cc_start: 0.7917 (t0) cc_final: 0.7702 (t0) REVERT: C 107 LEU cc_start: 0.8899 (tt) cc_final: 0.8552 (mm) REVERT: C 189 ILE cc_start: 0.9438 (mm) cc_final: 0.8936 (mm) REVERT: C 361 LEU cc_start: 0.9094 (pp) cc_final: 0.8464 (pp) REVERT: C 371 LEU cc_start: 0.8284 (tp) cc_final: 0.7642 (pp) REVERT: C 399 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8821 (mtmm) REVERT: C 403 MET cc_start: 0.8114 (mtt) cc_final: 0.7126 (tpt) REVERT: C 448 PHE cc_start: 0.6813 (m-80) cc_final: 0.6482 (m-80) REVERT: D 50 PHE cc_start: 0.7823 (t80) cc_final: 0.7003 (t80) REVERT: D 52 THR cc_start: 0.7295 (m) cc_final: 0.6952 (p) REVERT: D 53 TYR cc_start: 0.8626 (m-10) cc_final: 0.7985 (m-10) REVERT: D 58 PHE cc_start: 0.9179 (m-10) cc_final: 0.8911 (m-80) REVERT: D 213 ASP cc_start: 0.8937 (m-30) cc_final: 0.8502 (m-30) REVERT: D 999 MET cc_start: 0.7388 (tpt) cc_final: 0.7164 (tpt) REVERT: D 1018 GLN cc_start: 0.7097 (pm20) cc_final: 0.6893 (pm20) REVERT: E 270 MET cc_start: 0.9063 (ppp) cc_final: 0.8310 (ppp) REVERT: E 273 HIS cc_start: 0.8303 (m90) cc_final: 0.7962 (m90) REVERT: E 1002 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8107 (pm20) REVERT: E 1015 ASN cc_start: 0.7171 (m-40) cc_final: 0.6957 (t0) REVERT: E 1032 LEU cc_start: 0.9240 (mt) cc_final: 0.8932 (mt) REVERT: G 382 MET cc_start: 0.6618 (tmm) cc_final: 0.6417 (tmm) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2446 time to fit residues: 61.4296 Evaluate side-chains 116 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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: 10.0000 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 518 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 269 ASN ** G 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13279 Z= 0.218 Angle : 0.668 8.880 17873 Z= 0.343 Chirality : 0.043 0.166 2018 Planarity : 0.004 0.059 2276 Dihedral : 5.426 27.959 1735 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % 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: -1.18 (0.21), residues: 1583 helix: 0.06 (0.17), residues: 829 sheet: -0.54 (0.50), residues: 123 loop : -1.96 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 200 HIS 0.007 0.001 HIS B 201 PHE 0.021 0.002 PHE C 398 TYR 0.018 0.002 TYR C 111 ARG 0.009 0.001 ARG G 320 *********************** 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 153 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.9037 (tp) cc_final: 0.8797 (tt) REVERT: C 32 PHE cc_start: 0.9043 (m-80) cc_final: 0.8794 (m-80) REVERT: C 43 ASN cc_start: 0.7923 (t0) cc_final: 0.7644 (t0) REVERT: C 189 ILE cc_start: 0.9443 (mm) cc_final: 0.9043 (mp) REVERT: C 361 LEU cc_start: 0.9116 (pp) cc_final: 0.8531 (pp) REVERT: C 371 LEU cc_start: 0.8259 (tp) cc_final: 0.7796 (pp) REVERT: D 50 PHE cc_start: 0.7894 (t80) cc_final: 0.7063 (t80) REVERT: D 52 THR cc_start: 0.7214 (m) cc_final: 0.6889 (p) REVERT: D 53 TYR cc_start: 0.8649 (m-10) cc_final: 0.8030 (m-10) REVERT: D 58 PHE cc_start: 0.9182 (m-10) cc_final: 0.8924 (m-80) REVERT: D 213 ASP cc_start: 0.8932 (m-30) cc_final: 0.8499 (m-30) REVERT: D 999 MET cc_start: 0.7552 (tpt) cc_final: 0.7318 (tpt) REVERT: E 270 MET cc_start: 0.9068 (ppp) cc_final: 0.8318 (ppp) REVERT: E 273 HIS cc_start: 0.8425 (m90) cc_final: 0.8086 (m90) REVERT: E 1002 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8165 (mp0) REVERT: G 382 MET cc_start: 0.6845 (tmm) cc_final: 0.6551 (tmm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.2291 time to fit residues: 53.4826 Evaluate side-chains 112 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.627 ------------------------------------------------------------------------------- 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: 4.9990 chunk 142 optimal weight: 2.9990 chunk 146 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 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** ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.5273 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= 0.179 Angle : 0.651 11.625 17873 Z= 0.330 Chirality : 0.043 0.178 2018 Planarity : 0.004 0.053 2276 Dihedral : 5.226 27.297 1735 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.07 % Allowed : 0.97 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.21), residues: 1583 helix: 0.25 (0.18), residues: 834 sheet: -0.61 (0.52), residues: 113 loop : -1.90 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E1036 HIS 0.008 0.001 HIS B 328 PHE 0.029 0.002 PHE B 253 TYR 0.014 0.001 TYR C 472 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 160 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8988 (tp) cc_final: 0.8754 (tt) REVERT: B 396 PHE cc_start: 0.8354 (t80) cc_final: 0.7996 (t80) REVERT: B 416 TYR cc_start: 0.7987 (m-80) cc_final: 0.7635 (m-80) REVERT: B 433 PHE cc_start: 0.8148 (m-80) cc_final: 0.7564 (m-80) REVERT: C 32 PHE cc_start: 0.9008 (m-80) cc_final: 0.8751 (m-80) REVERT: C 43 ASN cc_start: 0.7821 (t0) cc_final: 0.7418 (t0) REVERT: C 189 ILE cc_start: 0.9408 (mm) cc_final: 0.8977 (mp) REVERT: C 361 LEU cc_start: 0.9135 (pp) cc_final: 0.8550 (pp) REVERT: D 50 PHE cc_start: 0.7880 (t80) cc_final: 0.7048 (t80) REVERT: D 52 THR cc_start: 0.7111 (m) cc_final: 0.6816 (p) REVERT: D 53 TYR cc_start: 0.8622 (m-10) cc_final: 0.8019 (m-10) REVERT: D 58 PHE cc_start: 0.9143 (m-10) cc_final: 0.8851 (m-80) REVERT: D 213 ASP cc_start: 0.8901 (m-30) cc_final: 0.8480 (m-30) REVERT: D 999 MET cc_start: 0.7578 (tpt) cc_final: 0.7353 (tpt) REVERT: D 1025 GLU cc_start: 0.8528 (mp0) cc_final: 0.8233 (mp0) REVERT: E 270 MET cc_start: 0.9082 (ppp) cc_final: 0.8353 (ppp) REVERT: E 273 HIS cc_start: 0.8351 (m90) cc_final: 0.8041 (m90) REVERT: E 1002 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8172 (mp0) REVERT: E 1015 ASN cc_start: 0.6826 (t0) cc_final: 0.6487 (t0) REVERT: E 1032 LEU cc_start: 0.9084 (mt) cc_final: 0.8672 (mt) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2341 time to fit residues: 56.5385 Evaluate side-chains 116 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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: 10.0000 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 77 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 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** ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.5445 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= 0.179 Angle : 0.648 11.755 17873 Z= 0.330 Chirality : 0.043 0.192 2018 Planarity : 0.004 0.053 2276 Dihedral : 5.178 27.241 1735 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % 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: -1.00 (0.21), residues: 1583 helix: 0.25 (0.18), residues: 823 sheet: -0.56 (0.52), residues: 113 loop : -1.87 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 240 HIS 0.007 0.001 HIS B 201 PHE 0.032 0.002 PHE B 399 TYR 0.016 0.001 TYR C 82 ARG 0.010 0.001 ARG E 933 ********************** 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 157 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 LEU cc_start: 0.8993 (tp) cc_final: 0.8748 (tt) REVERT: B 433 PHE cc_start: 0.8065 (m-80) cc_final: 0.7638 (m-80) REVERT: C 32 PHE cc_start: 0.8974 (m-80) cc_final: 0.8724 (m-80) REVERT: C 43 ASN cc_start: 0.7764 (t0) cc_final: 0.7342 (t0) REVERT: C 189 ILE cc_start: 0.9404 (mm) cc_final: 0.8953 (mp) REVERT: C 361 LEU cc_start: 0.9117 (pp) cc_final: 0.8557 (pp) REVERT: C 371 LEU cc_start: 0.8276 (tp) cc_final: 0.7693 (pp) REVERT: D 50 PHE cc_start: 0.7877 (t80) cc_final: 0.7044 (t80) REVERT: D 52 THR cc_start: 0.7012 (m) cc_final: 0.6738 (p) REVERT: D 53 TYR cc_start: 0.8672 (m-10) cc_final: 0.8090 (m-10) REVERT: D 58 PHE cc_start: 0.9116 (m-10) cc_final: 0.8831 (m-80) REVERT: D 213 ASP cc_start: 0.8883 (m-30) cc_final: 0.8475 (m-30) REVERT: D 999 MET cc_start: 0.7561 (tpt) cc_final: 0.7338 (tpt) REVERT: E 270 MET cc_start: 0.9074 (ppp) cc_final: 0.8341 (ppp) REVERT: E 273 HIS cc_start: 0.8404 (m90) cc_final: 0.8075 (m90) REVERT: E 977 MET cc_start: 0.7476 (tmm) cc_final: 0.7152 (tmm) REVERT: E 1002 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8176 (mp0) REVERT: E 1032 LEU cc_start: 0.9012 (mt) cc_final: 0.8682 (mt) REVERT: G 382 MET cc_start: 0.7439 (tmm) cc_final: 0.7235 (ppp) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.2279 time to fit residues: 54.4430 Evaluate side-chains 108 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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: 0.1980 chunk 116 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 110 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 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** ** G 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 GLN ** 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 = 0.4117 r_free = 0.4117 target = 0.097061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.078582 restraints weight = 89154.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.080166 restraints weight = 64735.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.082199 restraints weight = 45664.956| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13279 Z= 0.158 Angle : 0.628 11.606 17873 Z= 0.315 Chirality : 0.043 0.217 2018 Planarity : 0.004 0.052 2276 Dihedral : 5.012 27.019 1735 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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: -0.70 (0.21), residues: 1583 helix: 0.49 (0.18), residues: 815 sheet: -0.39 (0.50), residues: 123 loop : -1.72 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.030 0.002 PHE B 399 TYR 0.014 0.001 TYR C 412 ARG 0.017 0.001 ARG E 980 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2589.93 seconds wall clock time: 47 minutes 42.05 seconds (2862.05 seconds total)