Starting phenix.real_space_refine on Sat Jul 20 04:49:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u89_42018/07_2024/8u89_42018_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u89_42018/07_2024/8u89_42018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u89_42018/07_2024/8u89_42018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u89_42018/07_2024/8u89_42018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u89_42018/07_2024/8u89_42018_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u89_42018/07_2024/8u89_42018_neut.cif" } resolution = 3.3 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= 0.037 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: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 55 5.16 5 C 6361 2.51 5 N 1665 2.21 5 O 1845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 113": "NH1" <-> "NH2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9928 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3091 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 23, 'TRANS': 349} Chain: "C" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2430 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.45, per 1000 atoms: 0.55 Number of scatterers: 9928 At special positions: 0 Unit cell: (108.936, 113.208, 116.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 55 16.00 O 1845 8.00 N 1665 7.00 C 6361 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: 3.84 Conformation dependent library (CDL) restraints added in 1.7 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 3 sheets defined 75.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.937A pdb=" N GLY A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 5.602A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 88 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 101 through 119 removed outlier: 3.547A pdb=" N LYS A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.167A pdb=" N GLU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.713A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 194 removed outlier: 4.750A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.654A pdb=" N MET A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.096A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.540A pdb=" N LEU A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 292 removed outlier: 3.893A pdb=" N THR A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.750A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.863A pdb=" N CYS A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 335 removed outlier: 4.890A pdb=" N LEU A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix removed outlier: 3.604A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.820A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 351 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 357 through 374 removed outlier: 4.748A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 387 removed outlier: 4.009A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.870A pdb=" N VAL A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 416 through 435 Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.586A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 455 through 474 Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.643A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 494 through 521 removed outlier: 4.392A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 568 removed outlier: 4.233A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 138 through 159 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.953A pdb=" N ASP B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 removed outlier: 4.499A pdb=" N LEU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 236 through 246 removed outlier: 3.527A pdb=" N LEU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 269 Processing helix chain 'B' and resid 272 through 290 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 316 through 326 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.772A pdb=" N VAL B 333 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 4.221A pdb=" N TYR B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 357 through 368 Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 392 through 413 removed outlier: 3.547A pdb=" N SER B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Proline residue: B 402 - end of helix removed outlier: 3.693A pdb=" N LYS B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 438 through 453 Proline residue: B 444 - end of helix Proline residue: B 448 - end of helix removed outlier: 3.622A pdb=" N ASN B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 477 removed outlier: 3.533A pdb=" N HIS B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.588A pdb=" N LYS C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.729A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.530A pdb=" N ALA C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.698A pdb=" N ASP C 202 " --> pdb=" O PHE C 220 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1683 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: 3.21 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1831 1.33 - 1.45: 2460 1.45 - 1.57: 5768 1.57 - 1.70: 1 1.70 - 1.82: 82 Bond restraints: 10142 Sorted by residual: bond pdb=" C PRO A 276 " pdb=" O PRO A 276 " ideal model delta sigma weight residual 1.238 1.201 0.037 1.24e-02 6.50e+03 8.88e+00 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.37e+00 bond pdb=" N ASP A 293 " pdb=" CA ASP A 293 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.20e+00 bond pdb=" N GLU A 204 " pdb=" CA GLU A 204 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.25e-02 6.40e+03 8.15e+00 bond pdb=" N VAL A 274 " pdb=" CA VAL A 274 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.90e+00 ... (remaining 10137 not shown) Histogram of bond angle deviations from ideal: 100.11 - 106.91: 316 106.91 - 113.70: 5628 113.70 - 120.50: 4154 120.50 - 127.29: 3544 127.29 - 134.08: 115 Bond angle restraints: 13757 Sorted by residual: angle pdb=" N MET C 66 " pdb=" CA MET C 66 " pdb=" C MET C 66 " ideal model delta sigma weight residual 110.97 105.27 5.70 1.09e+00 8.42e-01 2.73e+01 angle pdb=" N ASN A 539 " pdb=" CA ASN A 539 " pdb=" C ASN A 539 " ideal model delta sigma weight residual 111.36 105.69 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" C GLN A 571 " pdb=" N ASP A 572 " pdb=" CA ASP A 572 " ideal model delta sigma weight residual 121.39 114.47 6.92 1.66e+00 3.63e-01 1.74e+01 angle pdb=" C GLU A 100 " pdb=" N GLU A 101 " pdb=" CA GLU A 101 " ideal model delta sigma weight residual 120.75 114.47 6.28 1.51e+00 4.39e-01 1.73e+01 angle pdb=" N MET A 499 " pdb=" CA MET A 499 " pdb=" C MET A 499 " ideal model delta sigma weight residual 111.82 107.24 4.58 1.16e+00 7.43e-01 1.56e+01 ... (remaining 13752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5360 17.91 - 35.82: 616 35.82 - 53.72: 154 53.72 - 71.63: 16 71.63 - 89.54: 13 Dihedral angle restraints: 6159 sinusoidal: 2502 harmonic: 3657 Sorted by residual: dihedral pdb=" CD ARG B 114 " pdb=" NE ARG B 114 " pdb=" CZ ARG B 114 " pdb=" NH1 ARG B 114 " ideal model delta sinusoidal sigma weight residual 0.00 -59.96 59.96 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CD ARG A 113 " pdb=" NE ARG A 113 " pdb=" CZ ARG A 113 " pdb=" NH1 ARG A 113 " ideal model delta sinusoidal sigma weight residual 0.00 -44.45 44.45 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CG ARG C 89 " pdb=" CD ARG C 89 " pdb=" NE ARG C 89 " pdb=" CZ ARG C 89 " ideal model delta sinusoidal sigma weight residual -90.00 -37.14 -52.86 2 1.50e+01 4.44e-03 1.36e+01 ... (remaining 6156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1234 0.050 - 0.100: 287 0.100 - 0.151: 35 0.151 - 0.201: 7 0.201 - 0.251: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB VAL C 159 " pdb=" CA VAL C 159 " pdb=" CG1 VAL C 159 " pdb=" CG2 VAL C 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE B 308 " pdb=" N ILE B 308 " pdb=" C ILE B 308 " pdb=" CB ILE B 308 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA LYS A 163 " pdb=" N LYS A 163 " pdb=" C LYS A 163 " pdb=" CB LYS A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 1561 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 114 " -0.953 9.50e-02 1.11e+02 4.27e-01 1.10e+02 pdb=" NE ARG B 114 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 114 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 114 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 114 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 113 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG A 113 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 113 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 113 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 113 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 273 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.37e+00 pdb=" C ALA A 273 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 273 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 274 " 0.016 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 120 2.65 - 3.21: 9438 3.21 - 3.78: 15969 3.78 - 4.34: 21181 4.34 - 4.90: 34820 Nonbonded interactions: 81528 Sorted by model distance: nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 2.091 2.320 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.136 2.320 nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 2.156 2.400 nonbonded pdb=" NE2 HIS C 167 " pdb="MN MN C 401 " model vdw 2.165 2.400 nonbonded pdb=" CD ARG B 114 " pdb=" OH TYR B 155 " model vdw 2.197 3.440 ... (remaining 81523 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 individual isotropic 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: 0.930 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.580 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 0.090 10142 Z= 0.219 Angle : 0.698 8.431 13757 Z= 0.400 Chirality : 0.043 0.251 1564 Planarity : 0.014 0.427 1767 Dihedral : 16.176 89.540 3779 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.54 % Allowed : 20.24 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1233 helix: 1.29 (0.19), residues: 810 sheet: -0.43 (0.94), residues: 37 loop : -0.51 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 417 HIS 0.003 0.000 HIS B 293 PHE 0.035 0.001 PHE B 396 TYR 0.015 0.001 TYR A 426 ARG 0.012 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 154 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.6736 (ttp-170) cc_final: 0.5824 (tpp-160) REVERT: A 226 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7757 (mt-10) REVERT: B 227 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8112 (tm-30) REVERT: B 317 GLU cc_start: 0.7091 (tp30) cc_final: 0.6817 (tp30) outliers start: 6 outliers final: 2 residues processed: 157 average time/residue: 0.2282 time to fit residues: 50.0028 Evaluate side-chains 134 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain C residue 131 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS B 406 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10142 Z= 0.179 Angle : 0.537 6.070 13757 Z= 0.270 Chirality : 0.040 0.144 1564 Planarity : 0.004 0.043 1767 Dihedral : 3.983 23.306 1342 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.18 % Allowed : 18.69 % Favored : 79.13 % 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: 1.25 (0.25), residues: 1233 helix: 1.57 (0.19), residues: 813 sheet: -0.87 (0.74), residues: 55 loop : -0.49 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 417 HIS 0.003 0.001 HIS B 293 PHE 0.029 0.001 PHE B 396 TYR 0.009 0.001 TYR A 495 ARG 0.006 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.6513 (ttp-170) cc_final: 0.5783 (mtt180) REVERT: A 195 VAL cc_start: 0.8725 (m) cc_final: 0.8274 (p) REVERT: A 226 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7819 (mt-10) REVERT: B 317 GLU cc_start: 0.7041 (tp30) cc_final: 0.6762 (tp30) outliers start: 24 outliers final: 12 residues processed: 160 average time/residue: 0.1921 time to fit residues: 44.9264 Evaluate side-chains 139 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10142 Z= 0.158 Angle : 0.521 6.343 13757 Z= 0.259 Chirality : 0.039 0.131 1564 Planarity : 0.004 0.037 1767 Dihedral : 3.783 18.535 1339 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.54 % Allowed : 18.42 % Favored : 79.04 % 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: 1.38 (0.25), residues: 1233 helix: 1.69 (0.19), residues: 814 sheet: -0.70 (0.72), residues: 53 loop : -0.54 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.002 0.000 HIS B 293 PHE 0.022 0.001 PHE B 396 TYR 0.009 0.001 TYR B 430 ARG 0.011 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8737 (m) cc_final: 0.8307 (p) REVERT: A 226 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7842 (mt-10) REVERT: B 215 GLU cc_start: 0.8711 (tp30) cc_final: 0.8424 (tp30) REVERT: B 244 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 474 MET cc_start: 0.8078 (mtp) cc_final: 0.7841 (mtm) REVERT: C 174 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5953 (tp) outliers start: 28 outliers final: 12 residues processed: 157 average time/residue: 0.1969 time to fit residues: 45.9698 Evaluate side-chains 138 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.0980 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 32 optimal weight: 0.0370 chunk 99 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10142 Z= 0.163 Angle : 0.521 6.898 13757 Z= 0.258 Chirality : 0.039 0.134 1564 Planarity : 0.004 0.039 1767 Dihedral : 3.758 18.128 1339 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.54 % Allowed : 19.42 % Favored : 78.04 % 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: 1.45 (0.25), residues: 1233 helix: 1.71 (0.19), residues: 815 sheet: -0.67 (0.72), residues: 53 loop : -0.44 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.002 0.000 HIS B 293 PHE 0.033 0.001 PHE B 396 TYR 0.009 0.001 TYR A 426 ARG 0.007 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8679 (m) cc_final: 0.8281 (p) REVERT: A 226 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7861 (mt-10) REVERT: A 350 MET cc_start: 0.8070 (mtt) cc_final: 0.7807 (mtt) REVERT: B 244 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8390 (mt) REVERT: B 474 MET cc_start: 0.8177 (mtp) cc_final: 0.7967 (mtm) REVERT: C 174 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6106 (tp) outliers start: 28 outliers final: 18 residues processed: 152 average time/residue: 0.1879 time to fit residues: 42.3660 Evaluate side-chains 145 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10142 Z= 0.209 Angle : 0.542 7.035 13757 Z= 0.269 Chirality : 0.040 0.133 1564 Planarity : 0.004 0.040 1767 Dihedral : 3.809 17.757 1339 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.81 % Allowed : 19.69 % Favored : 77.50 % 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: 1.42 (0.25), residues: 1233 helix: 1.70 (0.19), residues: 817 sheet: -0.49 (0.73), residues: 53 loop : -0.52 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 417 HIS 0.003 0.001 HIS B 463 PHE 0.024 0.001 PHE B 396 TYR 0.012 0.001 TYR A 495 ARG 0.003 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8763 (m) cc_final: 0.8389 (p) REVERT: A 226 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7745 (mt-10) REVERT: A 350 MET cc_start: 0.8259 (mtt) cc_final: 0.7695 (mtt) REVERT: A 388 LEU cc_start: 0.8904 (mt) cc_final: 0.8588 (mt) REVERT: A 487 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 244 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 474 MET cc_start: 0.8151 (mtp) cc_final: 0.7887 (mtm) REVERT: C 174 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6265 (tp) outliers start: 31 outliers final: 20 residues processed: 158 average time/residue: 0.1716 time to fit residues: 41.2577 Evaluate side-chains 147 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 98 optimal weight: 0.0980 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN C 229 ASN C 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10142 Z= 0.151 Angle : 0.524 7.932 13757 Z= 0.260 Chirality : 0.039 0.151 1564 Planarity : 0.003 0.033 1767 Dihedral : 3.719 17.758 1339 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.72 % Allowed : 19.96 % Favored : 77.31 % 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: 1.48 (0.25), residues: 1233 helix: 1.74 (0.19), residues: 816 sheet: -0.48 (0.74), residues: 53 loop : -0.47 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 417 HIS 0.003 0.000 HIS B 293 PHE 0.024 0.001 PHE B 396 TYR 0.011 0.001 TYR A 426 ARG 0.006 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8653 (m) cc_final: 0.8277 (p) REVERT: A 277 GLU cc_start: 0.8620 (tp30) cc_final: 0.7914 (tp30) REVERT: A 350 MET cc_start: 0.8275 (mtt) cc_final: 0.7760 (mtt) REVERT: B 114 ARG cc_start: 0.7148 (mtt-85) cc_final: 0.6406 (mtt-85) REVERT: B 244 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (mt) REVERT: B 452 ARG cc_start: 0.8825 (tmm-80) cc_final: 0.8618 (tmm-80) REVERT: B 455 LYS cc_start: 0.6340 (mmmt) cc_final: 0.6095 (mtmt) REVERT: B 470 LEU cc_start: 0.7142 (mt) cc_final: 0.6799 (mt) REVERT: B 474 MET cc_start: 0.8284 (mtp) cc_final: 0.8012 (mtm) REVERT: C 174 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6382 (tp) outliers start: 30 outliers final: 23 residues processed: 160 average time/residue: 0.1733 time to fit residues: 42.4464 Evaluate side-chains 151 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 255 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 229 ASN C 249 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10142 Z= 0.171 Angle : 0.533 7.463 13757 Z= 0.264 Chirality : 0.039 0.151 1564 Planarity : 0.003 0.033 1767 Dihedral : 3.722 17.525 1339 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.63 % Allowed : 20.51 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1233 helix: 1.73 (0.19), residues: 817 sheet: -0.58 (0.73), residues: 53 loop : -0.49 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 417 HIS 0.003 0.001 HIS B 293 PHE 0.037 0.001 PHE B 396 TYR 0.012 0.001 TYR A 426 ARG 0.005 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6612 (mt) REVERT: A 195 VAL cc_start: 0.8675 (m) cc_final: 0.8311 (p) REVERT: A 277 GLU cc_start: 0.8560 (tp30) cc_final: 0.7866 (tp30) REVERT: A 350 MET cc_start: 0.8283 (mtt) cc_final: 0.7708 (mtt) REVERT: A 388 LEU cc_start: 0.8920 (mt) cc_final: 0.8585 (mt) REVERT: B 114 ARG cc_start: 0.7314 (mtt-85) cc_final: 0.6557 (mtt-85) REVERT: B 244 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8420 (mt) REVERT: B 470 LEU cc_start: 0.7166 (mt) cc_final: 0.6831 (mt) REVERT: B 474 MET cc_start: 0.8281 (mtp) cc_final: 0.8007 (mtm) REVERT: C 174 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6343 (tp) outliers start: 29 outliers final: 23 residues processed: 148 average time/residue: 0.1730 time to fit residues: 39.0922 Evaluate side-chains 150 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 175 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 11 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 113 optimal weight: 0.3980 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10142 Z= 0.135 Angle : 0.520 8.038 13757 Z= 0.255 Chirality : 0.038 0.138 1564 Planarity : 0.003 0.034 1767 Dihedral : 3.623 17.384 1339 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.09 % Allowed : 21.14 % Favored : 76.77 % 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: 1.54 (0.25), residues: 1233 helix: 1.77 (0.19), residues: 820 sheet: -0.68 (0.73), residues: 53 loop : -0.39 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 417 HIS 0.003 0.000 HIS B 293 PHE 0.034 0.001 PHE B 396 TYR 0.013 0.001 TYR A 426 ARG 0.004 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 124 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6370 (mt) REVERT: A 180 MET cc_start: 0.8621 (mpp) cc_final: 0.8363 (mpp) REVERT: A 195 VAL cc_start: 0.8628 (m) cc_final: 0.8275 (p) REVERT: A 277 GLU cc_start: 0.8305 (tp30) cc_final: 0.7770 (tp30) REVERT: A 350 MET cc_start: 0.8303 (mtt) cc_final: 0.7769 (mtt) REVERT: B 174 MET cc_start: 0.7277 (tmm) cc_final: 0.7058 (tmm) REVERT: B 474 MET cc_start: 0.8083 (mtp) cc_final: 0.7841 (mtm) REVERT: C 174 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6482 (tp) outliers start: 23 outliers final: 18 residues processed: 160 average time/residue: 0.1840 time to fit residues: 44.4520 Evaluate side-chains 148 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN C 255 ASN C 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10142 Z= 0.204 Angle : 0.551 8.076 13757 Z= 0.272 Chirality : 0.040 0.160 1564 Planarity : 0.003 0.034 1767 Dihedral : 3.704 17.527 1339 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.81 % Allowed : 20.78 % Favored : 76.41 % 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: 1.47 (0.25), residues: 1233 helix: 1.72 (0.19), residues: 820 sheet: -0.67 (0.74), residues: 53 loop : -0.42 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.004 0.001 HIS B 293 PHE 0.030 0.001 PHE B 396 TYR 0.013 0.001 TYR A 426 ARG 0.004 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.251 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8642 (m) cc_final: 0.8312 (p) REVERT: A 277 GLU cc_start: 0.8342 (tp30) cc_final: 0.7770 (tp30) REVERT: A 350 MET cc_start: 0.8261 (mtt) cc_final: 0.7681 (mtt) REVERT: A 388 LEU cc_start: 0.8929 (mt) cc_final: 0.8590 (mt) REVERT: A 487 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8488 (mp) REVERT: B 244 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8445 (mt) REVERT: B 474 MET cc_start: 0.8061 (mtp) cc_final: 0.7859 (mtm) outliers start: 31 outliers final: 23 residues processed: 149 average time/residue: 0.1840 time to fit residues: 41.2815 Evaluate side-chains 147 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 255 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN C 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 10142 Z= 0.251 Angle : 0.856 59.199 13757 Z= 0.479 Chirality : 0.039 0.123 1564 Planarity : 0.004 0.047 1767 Dihedral : 3.697 17.549 1339 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.72 % Allowed : 20.96 % Favored : 76.32 % 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: 1.49 (0.25), residues: 1233 helix: 1.73 (0.19), residues: 820 sheet: -0.69 (0.74), residues: 53 loop : -0.40 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.004 0.001 HIS C 179 PHE 0.029 0.001 PHE B 396 TYR 0.012 0.001 TYR A 426 ARG 0.005 0.000 ARG C 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.207 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8641 (m) cc_final: 0.8311 (p) REVERT: A 277 GLU cc_start: 0.8341 (tp30) cc_final: 0.7764 (tp30) REVERT: A 350 MET cc_start: 0.8261 (mtt) cc_final: 0.7671 (mtt) REVERT: A 388 LEU cc_start: 0.8925 (mt) cc_final: 0.8587 (mt) REVERT: A 487 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8483 (mp) REVERT: B 244 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8442 (mt) REVERT: B 474 MET cc_start: 0.8063 (mtp) cc_final: 0.7859 (mtm) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.1791 time to fit residues: 39.1178 Evaluate side-chains 149 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.0970 chunk 89 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.0770 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.140039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115724 restraints weight = 17569.677| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.56 r_work: 0.3453 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 10142 Z= 0.251 Angle : 0.856 59.199 13757 Z= 0.479 Chirality : 0.039 0.123 1564 Planarity : 0.004 0.047 1767 Dihedral : 3.697 17.549 1339 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.45 % Allowed : 21.14 % Favored : 76.41 % 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: 1.49 (0.25), residues: 1233 helix: 1.73 (0.19), residues: 820 sheet: -0.69 (0.74), residues: 53 loop : -0.40 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.004 0.001 HIS C 179 PHE 0.029 0.001 PHE B 396 TYR 0.012 0.001 TYR A 426 ARG 0.005 0.000 ARG C 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.87 seconds wall clock time: 39 minutes 17.03 seconds (2357.03 seconds total)