Starting phenix.real_space_refine on Sun Dec 10 02:11:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/12_2023/8t8f_41098_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/12_2023/8t8f_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_41098/12_2023/8t8f_41098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/12_2023/8t8f_41098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/12_2023/8t8f_41098_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t8f_41098/12_2023/8t8f_41098_neut.pdb" } 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-1.21rc1-5172/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: 6.73, per 1000 atoms: 0.52 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: 5.33 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: 1.24 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: 3.49 Time building geometry restraints manager: 5.71 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: 5.140 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: 12.510 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 34.890 Find NCS groups from input model: 0.400 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.240 ------------------------------------------------------------------------------- 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 : 1.534 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 outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.2417 time to fit residues: 66.8278 Evaluate side-chains 132 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9537 ------------------------------------------------------------------------------- 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: 0.0270 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 64 optimal weight: 5.9990 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: 0.3896 ------------------------------------------------------------------------------- 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 221 ASN 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** G 376 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13279 Z= 0.155 Angle : 0.595 9.676 17873 Z= 0.307 Chirality : 0.042 0.188 2018 Planarity : 0.004 0.053 2276 Dihedral : 5.084 32.533 1735 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.45 % 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: -0.47 (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 0.015 0.002 PHE D1010 TYR 0.013 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 186 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.657 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 outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2678 time to fit residues: 72.5322 Evaluate side-chains 138 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.713 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2830 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 143 optimal weight: 0.0670 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN C 109 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN D 226 GLN ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2243 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= 0.252 Angle : 0.680 8.454 17873 Z= 0.356 Chirality : 0.044 0.265 2018 Planarity : 0.004 0.046 2276 Dihedral : 5.235 31.368 1735 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.21 % Allowed : 4.49 % Favored : 95.31 % 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: -1.10 (0.21), residues: 1583 helix: 0.31 (0.18), residues: 812 sheet: -0.81 (0.44), residues: 133 loop : -2.09 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 200 HIS 0.010 0.002 HIS C 513 PHE 0.025 0.002 PHE E 230 TYR 0.021 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 169 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 2.400 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 outliers start: 3 outliers final: 1 residues processed: 168 average time/residue: 0.2708 time to fit residues: 68.4029 Evaluate side-chains 121 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.602 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1774 time to fit residues: 2.5698 ------------------------------------------------------------------------------- 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: 0.8980 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 HIS C 109 GLN 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** ** D1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13279 Z= 0.179 Angle : 0.611 10.456 17873 Z= 0.315 Chirality : 0.042 0.165 2018 Planarity : 0.004 0.047 2276 Dihedral : 5.092 30.610 1735 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.14 % Favored : 92.80 % Rotamer: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % 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: -0.92 (0.21), residues: 1583 helix: 0.46 (0.18), residues: 806 sheet: -0.80 (0.47), residues: 123 loop : -1.94 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 220 HIS 0.009 0.001 HIS C 513 PHE 0.022 0.002 PHE C 398 TYR 0.010 0.001 TYR C 82 ARG 0.005 0.001 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 169 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 168 average time/residue: 0.2457 time to fit residues: 61.4227 Evaluate side-chains 120 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3391 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 106 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 HIS 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 158 ASN ** 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: 0.6720 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13279 Z= 0.219 Angle : 0.632 9.662 17873 Z= 0.330 Chirality : 0.042 0.142 2018 Planarity : 0.004 0.049 2276 Dihedral : 5.126 27.545 1735 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.53 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.87 (0.21), residues: 1583 helix: 0.42 (0.18), residues: 816 sheet: -0.43 (0.50), residues: 123 loop : -1.93 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 200 HIS 0.008 0.002 HIS C 513 PHE 0.021 0.002 PHE E 230 TYR 0.018 0.002 TYR C 307 ARG 0.005 0.001 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 164 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2408 time to fit residues: 59.2004 Evaluate side-chains 114 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2745 ------------------------------------------------------------------------------- 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: 8.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 0.1980 chunk 153 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 0.0010 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.0570 chunk 148 optimal weight: 9.9990 overall best weight: 0.3906 ------------------------------------------------------------------------------- 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 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13279 Z= 0.153 Angle : 0.603 9.797 17873 Z= 0.304 Chirality : 0.042 0.174 2018 Planarity : 0.004 0.102 2276 Dihedral : 4.934 31.676 1735 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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: -0.68 (0.21), residues: 1583 helix: 0.60 (0.18), residues: 817 sheet: -0.27 (0.50), residues: 125 loop : -1.88 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E1036 HIS 0.008 0.001 HIS C 513 PHE 0.021 0.001 PHE B 356 TYR 0.020 0.001 TYR E 284 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 176 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2300 time to fit residues: 61.6162 Evaluate side-chains 117 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2546 ------------------------------------------------------------------------------- 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: 0.7980 chunk 87 optimal weight: 0.0870 chunk 112 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.3761 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= 0.164 Angle : 0.621 10.863 17873 Z= 0.310 Chirality : 0.042 0.167 2018 Planarity : 0.004 0.063 2276 Dihedral : 4.855 27.562 1735 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.55 % 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: -0.68 (0.21), residues: 1583 helix: 0.58 (0.18), residues: 818 sheet: -0.30 (0.50), residues: 125 loop : -1.86 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.023 0.002 PHE B 411 TYR 0.018 0.001 TYR B 416 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 173 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2525 time to fit residues: 65.4325 Evaluate side-chains 119 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2719 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 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 359 HIS C 43 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** 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** ** E1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 324 ASN G 375 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13279 Z= 0.250 Angle : 0.717 9.472 17873 Z= 0.369 Chirality : 0.044 0.211 2018 Planarity : 0.005 0.060 2276 Dihedral : 5.345 27.309 1735 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.65 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1583 helix: 0.20 (0.18), residues: 824 sheet: -0.72 (0.49), residues: 125 loop : -1.87 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP B 200 HIS 0.007 0.002 HIS B 368 PHE 0.023 0.002 PHE B 399 TYR 0.026 0.002 TYR C 44 ARG 0.011 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 162 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2428 time to fit residues: 59.7038 Evaluate side-chains 110 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2318 ------------------------------------------------------------------------------- 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: 0.7980 chunk 142 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 134 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 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: 0.6695 moved from start: 0.4618 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= 0.165 Angle : 0.640 11.859 17873 Z= 0.317 Chirality : 0.042 0.156 2018 Planarity : 0.004 0.051 2276 Dihedral : 4.976 25.033 1735 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.68 (0.21), residues: 1583 helix: 0.52 (0.18), residues: 821 sheet: -0.53 (0.50), residues: 125 loop : -1.71 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.029 0.002 PHE B 399 TYR 0.014 0.001 TYR C 472 ARG 0.012 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 161 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.666 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 outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2333 time to fit residues: 56.8918 Evaluate side-chains 118 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.573 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1688 ------------------------------------------------------------------------------- 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: 0.9980 chunk 104 optimal weight: 8.9990 chunk 158 optimal weight: 0.0670 chunk 145 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 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: 0.6704 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13279 Z= 0.162 Angle : 0.626 11.829 17873 Z= 0.311 Chirality : 0.042 0.201 2018 Planarity : 0.004 0.044 2276 Dihedral : 4.835 25.242 1735 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.57 (0.22), residues: 1583 helix: 0.61 (0.18), residues: 822 sheet: -0.43 (0.50), residues: 125 loop : -1.67 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.028 0.002 PHE B 253 TYR 0.013 0.001 TYR C 82 ARG 0.012 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 160 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2305 time to fit residues: 57.4709 Evaluate side-chains 113 residues out of total 1484 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3758 ------------------------------------------------------------------------------- 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: 0.3980 chunk 116 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 52 optimal weight: 0.0970 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 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 = 0.4136 r_free = 0.4136 target = 0.098150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.079469 restraints weight = 87715.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.080820 restraints weight = 63317.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.081945 restraints weight = 48862.635| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13279 Z= 0.174 Angle : 0.624 11.716 17873 Z= 0.313 Chirality : 0.043 0.185 2018 Planarity : 0.004 0.045 2276 Dihedral : 4.852 25.049 1735 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.45 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % 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: -0.52 (0.22), residues: 1583 helix: 0.65 (0.18), residues: 823 sheet: -0.45 (0.50), residues: 125 loop : -1.65 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 200 HIS 0.007 0.001 HIS C 513 PHE 0.024 0.002 PHE B 399 TYR 0.016 0.001 TYR C 82 ARG 0.011 0.001 ARG E 980 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2580.80 seconds wall clock time: 48 minutes 27.44 seconds (2907.44 seconds total)