Starting phenix.real_space_refine on Thu Feb 5 09:09:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxq_61875/02_2026/9jxq_61875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxq_61875/02_2026/9jxq_61875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxq_61875/02_2026/9jxq_61875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxq_61875/02_2026/9jxq_61875.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxq_61875/02_2026/9jxq_61875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxq_61875/02_2026/9jxq_61875.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.023 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 76 5.16 5 C 10394 2.51 5 N 2742 2.21 5 O 2882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16094 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5055 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 20, 'TRANS': 588} Chain breaks: 2 Chain: "B" Number of atoms: 5055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5055 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 20, 'TRANS': 588} Chain breaks: 2 Chain: "C" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2992 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 12, 'TRANS': 377} Chain breaks: 1 Chain: "D" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2992 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 12, 'TRANS': 377} Chain breaks: 1 Time building chain proxies: 3.72, per 1000 atoms: 0.23 Number of scatterers: 16094 At special positions: 0 Unit cell: (126.6, 181.46, 142.425, 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 76 16.00 O 2882 8.00 N 2742 7.00 C 10394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 819.5 milliseconds 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 0 sheets defined 72.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 removed outlier: 4.184A pdb=" N HIS A 10 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 21 through 35 Processing helix chain 'A' and resid 43 through 100 removed outlier: 3.524A pdb=" N VAL A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 168 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.758A pdb=" N GLN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.742A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.824A pdb=" N ILE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.910A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 360 removed outlier: 3.666A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 390 through 419 removed outlier: 6.239A pdb=" N VAL A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 476 through 503 removed outlier: 3.831A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 533 removed outlier: 3.946A pdb=" N VAL A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 581 Processing helix chain 'A' and resid 591 through 619 Proline residue: A 598 - end of helix Processing helix chain 'A' and resid 637 through 642 removed outlier: 3.983A pdb=" N LEU A 641 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 11 removed outlier: 4.184A pdb=" N HIS B 10 " --> pdb=" O HIS B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 43 through 100 removed outlier: 3.524A pdb=" N VAL B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 168 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.758A pdb=" N GLN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.742A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 3.823A pdb=" N ILE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.910A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.666A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 419 removed outlier: 6.239A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 473 through 503 removed outlier: 3.577A pdb=" N LEU B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 533 removed outlier: 3.946A pdb=" N VAL B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 581 Processing helix chain 'B' and resid 591 through 619 Proline residue: B 598 - end of helix Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.983A pdb=" N LEU B 641 " --> pdb=" O ASP B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 48 removed outlier: 3.669A pdb=" N ILE C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU C 47 " --> pdb=" O MET C 43 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN C 48 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 73 through 82 removed outlier: 3.578A pdb=" N SER C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 116 through 127 removed outlier: 3.915A pdb=" N VAL C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LEU C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 148 Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 172 through 180 removed outlier: 4.282A pdb=" N LYS C 180 " --> pdb=" O TRP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.859A pdb=" N MET C 192 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 271 through 280 Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.540A pdb=" N LYS C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 313 Processing helix chain 'C' and resid 314 through 324 removed outlier: 3.642A pdb=" N CYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 347 through 358 removed outlier: 3.509A pdb=" N LYS C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 358 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 removed outlier: 4.089A pdb=" N ILE C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 378 " --> pdb=" O ILE C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 387 removed outlier: 3.597A pdb=" N ALA C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 406 through 414 removed outlier: 4.138A pdb=" N ILE C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.534A pdb=" N ILE C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 48 removed outlier: 4.191A pdb=" N GLU D 47 " --> pdb=" O MET D 43 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN D 48 " --> pdb=" O ILE D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.555A pdb=" N GLU D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 116 through 127 removed outlier: 3.852A pdb=" N VAL D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 148 Processing helix chain 'D' and resid 149 through 159 Processing helix chain 'D' and resid 172 through 180 removed outlier: 4.176A pdb=" N LYS D 180 " --> pdb=" O TRP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.872A pdb=" N MET D 192 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 248 through 259 Processing helix chain 'D' and resid 271 through 280 Processing helix chain 'D' and resid 281 through 291 removed outlier: 3.669A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 313 Processing helix chain 'D' and resid 314 through 324 removed outlier: 3.753A pdb=" N CYS D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 346 Processing helix chain 'D' and resid 347 through 358 removed outlier: 3.720A pdb=" N ASP D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS D 357 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 removed outlier: 4.286A pdb=" N ILE D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 387 removed outlier: 4.161A pdb=" N GLU D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 417 through 426 removed outlier: 4.102A pdb=" N GLN D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2940 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: 2.46 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2670 1.32 - 1.44: 4455 1.44 - 1.56: 9225 1.56 - 1.69: 0 1.69 - 1.81: 114 Bond restraints: 16464 Sorted by residual: bond pdb=" N VAL D 364 " pdb=" CA VAL D 364 " ideal model delta sigma weight residual 1.459 1.513 -0.054 1.25e-02 6.40e+03 1.84e+01 bond pdb=" N VAL C 364 " pdb=" CA VAL C 364 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N LEU D 396 " pdb=" CA LEU D 396 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" C ASN A 619 " pdb=" O ASN A 619 " ideal model delta sigma weight residual 1.235 1.199 0.037 1.26e-02 6.30e+03 8.51e+00 bond pdb=" N ASN B 619 " pdb=" CA ASN B 619 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.52e+00 ... (remaining 16459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 21696 1.55 - 3.09: 495 3.09 - 4.64: 89 4.64 - 6.18: 25 6.18 - 7.73: 5 Bond angle restraints: 22310 Sorted by residual: angle pdb=" N ASN A 619 " pdb=" CA ASN A 619 " pdb=" CB ASN A 619 " ideal model delta sigma weight residual 110.49 117.87 -7.38 1.69e+00 3.50e-01 1.91e+01 angle pdb=" CA ASN B 619 " pdb=" C ASN B 619 " pdb=" O ASN B 619 " ideal model delta sigma weight residual 120.51 114.94 5.57 1.43e+00 4.89e-01 1.52e+01 angle pdb=" C ASN B 619 " pdb=" CA ASN B 619 " pdb=" CB ASN B 619 " ideal model delta sigma weight residual 110.42 102.69 7.73 1.99e+00 2.53e-01 1.51e+01 angle pdb=" CA ASN A 619 " pdb=" C ASN A 619 " pdb=" O ASN A 619 " ideal model delta sigma weight residual 120.51 115.28 5.23 1.43e+00 4.89e-01 1.34e+01 angle pdb=" N ASN B 619 " pdb=" CA ASN B 619 " pdb=" CB ASN B 619 " ideal model delta sigma weight residual 110.49 116.42 -5.93 1.69e+00 3.50e-01 1.23e+01 ... (remaining 22305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 8847 16.39 - 32.78: 722 32.78 - 49.16: 142 49.16 - 65.55: 43 65.55 - 81.94: 4 Dihedral angle restraints: 9758 sinusoidal: 3924 harmonic: 5834 Sorted by residual: dihedral pdb=" CA GLU B 643 " pdb=" C GLU B 643 " pdb=" N GLN B 644 " pdb=" CA GLN B 644 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLU A 643 " pdb=" C GLU A 643 " pdb=" N GLN A 644 " pdb=" CA GLN A 644 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR C 261 " pdb=" C TYR C 261 " pdb=" N VAL C 262 " pdb=" CA VAL C 262 " ideal model delta harmonic sigma weight residual 180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 9755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1761 0.041 - 0.081: 612 0.081 - 0.122: 109 0.122 - 0.163: 11 0.163 - 0.203: 3 Chirality restraints: 2496 Sorted by residual: chirality pdb=" CB VAL D 364 " pdb=" CA VAL D 364 " pdb=" CG1 VAL D 364 " pdb=" CG2 VAL D 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU B 547 " pdb=" CB LEU B 547 " pdb=" CD1 LEU B 547 " pdb=" CD2 LEU B 547 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CG LEU A 547 " pdb=" CB LEU A 547 " pdb=" CD1 LEU A 547 " pdb=" CD2 LEU A 547 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 2493 not shown) Planarity restraints: 2822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 618 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ASN A 618 " -0.069 2.00e-02 2.50e+03 pdb=" O ASN A 618 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN A 619 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 618 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C ASN B 618 " -0.063 2.00e-02 2.50e+03 pdb=" O ASN B 618 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN B 619 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 129 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO C 130 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 130 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 130 " 0.027 5.00e-02 4.00e+02 ... (remaining 2819 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2081 2.75 - 3.29: 16254 3.29 - 3.82: 26438 3.82 - 4.36: 29716 4.36 - 4.90: 51515 Nonbonded interactions: 126004 Sorted by model distance: nonbonded pdb=" O ASP B 647 " pdb=" OH TYR D 113 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASP C 68 " pdb=" N LEU C 69 " model vdw 2.281 3.120 nonbonded pdb=" NH2 ARG A 270 " pdb=" OD2 ASP A 590 " model vdw 2.291 3.120 nonbonded pdb=" NH2 ARG B 270 " pdb=" OD2 ASP B 590 " model vdw 2.291 3.120 nonbonded pdb=" N ASP A 637 " pdb=" OH TYR C 169 " model vdw 2.293 3.120 ... (remaining 125999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 7.210 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.620 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2156 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 : 0.004 0.054 16464 Z= 0.188 Angle : 0.599 7.730 22310 Z= 0.328 Chirality : 0.040 0.203 2496 Planarity : 0.004 0.048 2822 Dihedral : 12.887 81.941 5990 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.80 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 1978 helix: 1.56 (0.14), residues: 1343 sheet: None (None), residues: 0 loop : -1.68 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 459 TYR 0.016 0.002 TYR B 524 PHE 0.026 0.002 PHE B 605 TRP 0.021 0.002 TRP B 607 HIS 0.008 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00408 (16464) covalent geometry : angle 0.59893 (22310) hydrogen bonds : bond 0.12675 ( 980) hydrogen bonds : angle 5.34741 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 476 HIS cc_start: 0.1681 (m90) cc_final: 0.1393 (m-70) REVERT: C 109 MET cc_start: 0.3035 (mtt) cc_final: 0.2436 (tpp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1397 time to fit residues: 48.0218 Evaluate side-chains 138 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 299 HIS A 616 HIS A 619 ASN A 639 GLN B 150 ASN B 288 ASN B 399 GLN B 479 ASN B 608 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 63 ASN C 71 ASN C 188 HIS C 202 ASN D 149 HIS D 237 ASN D 290 GLN D 373 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.178332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.161641 restraints weight = 43896.344| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 2.19 r_work: 0.4573 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3948 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16464 Z= 0.221 Angle : 0.755 8.505 22310 Z= 0.404 Chirality : 0.045 0.248 2496 Planarity : 0.007 0.073 2822 Dihedral : 4.795 19.915 2174 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.36 % Favored : 94.54 % Rotamer: Outliers : 1.34 % Allowed : 6.68 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 1978 helix: 0.76 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.032 0.003 TYR B 139 PHE 0.029 0.003 PHE A 382 TRP 0.049 0.003 TRP B 457 HIS 0.011 0.002 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00478 (16464) covalent geometry : angle 0.75522 (22310) hydrogen bonds : bond 0.05170 ( 980) hydrogen bonds : angle 4.90694 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 SER cc_start: 0.6077 (m) cc_final: 0.5733 (p) REVERT: A 461 ILE cc_start: 0.5884 (pt) cc_final: 0.5423 (mt) REVERT: A 552 VAL cc_start: 0.2463 (t) cc_final: 0.2222 (p) REVERT: B 6 HIS cc_start: 0.2677 (p-80) cc_final: 0.2301 (m90) REVERT: C 102 MET cc_start: 0.5480 (mtp) cc_final: 0.5269 (mtm) REVERT: C 192 MET cc_start: 0.2637 (mmm) cc_final: 0.2222 (mtp) REVERT: C 237 ASN cc_start: 0.4279 (t0) cc_final: 0.3887 (t0) REVERT: D 121 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7813 (tm-30) REVERT: D 222 ILE cc_start: 0.1990 (OUTLIER) cc_final: 0.1602 (mt) outliers start: 23 outliers final: 10 residues processed: 224 average time/residue: 0.1318 time to fit residues: 44.3660 Evaluate side-chains 165 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 408 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 160 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 57 optimal weight: 0.0970 chunk 130 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 116 optimal weight: 0.2980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 149 GLN A 399 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN C 421 GLN D 50 ASN D 71 ASN ** D 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.177732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.161617 restraints weight = 47402.848| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 2.19 r_work: 0.4513 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4509 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16464 Z= 0.159 Angle : 0.582 13.891 22310 Z= 0.309 Chirality : 0.039 0.196 2496 Planarity : 0.005 0.064 2822 Dihedral : 4.162 16.938 2174 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.85 % Rotamer: Outliers : 1.45 % Allowed : 10.05 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1978 helix: 1.34 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -1.67 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 459 TYR 0.022 0.002 TYR B 139 PHE 0.021 0.002 PHE A 460 TRP 0.030 0.002 TRP A 395 HIS 0.007 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00348 (16464) covalent geometry : angle 0.58244 (22310) hydrogen bonds : bond 0.04550 ( 980) hydrogen bonds : angle 4.50392 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.5618 (m-80) cc_final: 0.5387 (m-80) REVERT: A 65 GLU cc_start: 0.3627 (mm-30) cc_final: 0.3013 (tp30) REVERT: A 421 LEU cc_start: 0.6082 (tt) cc_final: 0.5023 (mt) REVERT: A 564 ILE cc_start: 0.0099 (OUTLIER) cc_final: -0.0510 (tt) REVERT: B 605 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6831 (p90) REVERT: B 646 MET cc_start: 0.3533 (pmm) cc_final: 0.1481 (tpp) REVERT: C 102 MET cc_start: 0.5224 (mtp) cc_final: 0.4975 (mtm) REVERT: C 109 MET cc_start: 0.2974 (mtt) cc_final: 0.2083 (ttp) REVERT: C 192 MET cc_start: 0.2703 (mmm) cc_final: 0.2227 (mtp) REVERT: C 204 MET cc_start: 0.4496 (mpp) cc_final: 0.3643 (mpp) REVERT: C 345 MET cc_start: 0.1564 (ptt) cc_final: 0.0418 (ppp) REVERT: D 121 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7785 (tm-30) REVERT: D 414 HIS cc_start: 0.5349 (t-90) cc_final: 0.4951 (t-170) outliers start: 25 outliers final: 10 residues processed: 206 average time/residue: 0.1270 time to fit residues: 39.9040 Evaluate side-chains 159 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain D residue 85 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.0060 chunk 28 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 177 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS A 294 GLN A 614 ASN A 616 HIS B 146 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.174087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.155073 restraints weight = 42255.020| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 2.34 r_work: 0.4349 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5433 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16464 Z= 0.199 Angle : 0.653 11.710 22310 Z= 0.346 Chirality : 0.041 0.230 2496 Planarity : 0.005 0.052 2822 Dihedral : 4.357 18.911 2174 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.16 % Favored : 94.69 % Rotamer: Outliers : 2.26 % Allowed : 12.20 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1978 helix: 1.09 (0.14), residues: 1350 sheet: None (None), residues: 0 loop : -1.79 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 459 TYR 0.037 0.002 TYR A 368 PHE 0.039 0.003 PHE A 58 TRP 0.050 0.003 TRP A 175 HIS 0.013 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00430 (16464) covalent geometry : angle 0.65294 (22310) hydrogen bonds : bond 0.04831 ( 980) hydrogen bonds : angle 4.57986 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 297 VAL cc_start: 0.8082 (t) cc_final: 0.7837 (t) REVERT: A 317 PHE cc_start: 0.7285 (m-10) cc_final: 0.7023 (m-10) REVERT: A 410 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7283 (mp) REVERT: A 421 LEU cc_start: 0.6835 (tt) cc_final: 0.5808 (mt) REVERT: B 417 TYR cc_start: 0.7512 (m-80) cc_final: 0.7203 (m-80) REVERT: B 528 TRP cc_start: 0.6516 (t-100) cc_final: 0.6214 (t-100) REVERT: B 577 ILE cc_start: 0.5913 (mm) cc_final: 0.5668 (mm) REVERT: B 612 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8077 (mm) REVERT: B 617 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7509 (mp) REVERT: B 646 MET cc_start: 0.3304 (pmm) cc_final: 0.3036 (pmm) REVERT: C 192 MET cc_start: 0.2674 (mmm) cc_final: 0.2290 (mtp) REVERT: C 345 MET cc_start: 0.1096 (ptt) cc_final: 0.0060 (ppp) REVERT: D 121 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7771 (tm-30) REVERT: D 345 MET cc_start: 0.6390 (mmt) cc_final: 0.5660 (ptt) outliers start: 39 outliers final: 18 residues processed: 219 average time/residue: 0.1270 time to fit residues: 42.3165 Evaluate side-chains 168 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 154 HIS Chi-restraints excluded: chain D residue 348 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 197 optimal weight: 8.9990 chunk 188 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 0.1980 chunk 125 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 248 ASN A 614 ASN B 60 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS B 399 GLN B 608 ASN ** D 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.172805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.153805 restraints weight = 43360.183| |-----------------------------------------------------------------------------| r_work (start): 0.4552 rms_B_bonded: 2.86 r_work: 0.4249 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 0.9485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16464 Z= 0.169 Angle : 0.615 12.483 22310 Z= 0.319 Chirality : 0.039 0.159 2496 Planarity : 0.005 0.056 2822 Dihedral : 4.158 17.343 2174 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 2.50 % Allowed : 14.23 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 1978 helix: 1.18 (0.14), residues: 1354 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 217 TYR 0.033 0.002 TYR A 368 PHE 0.024 0.002 PHE B 391 TRP 0.022 0.002 TRP A 534 HIS 0.009 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00379 (16464) covalent geometry : angle 0.61533 (22310) hydrogen bonds : bond 0.04738 ( 980) hydrogen bonds : angle 4.48829 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7801 (p) REVERT: A 369 LYS cc_start: 0.5585 (tmtt) cc_final: 0.5260 (tmtt) REVERT: A 410 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 421 LEU cc_start: 0.6810 (tt) cc_final: 0.5932 (mt) REVERT: B 308 ARG cc_start: 0.5354 (tpm170) cc_final: 0.4295 (ptp-170) REVERT: B 417 TYR cc_start: 0.7623 (m-80) cc_final: 0.7352 (m-80) REVERT: B 468 ARG cc_start: 0.4878 (mmp80) cc_final: 0.3416 (ttm170) REVERT: B 646 MET cc_start: 0.3100 (pmm) cc_final: 0.2867 (pmm) REVERT: C 43 MET cc_start: -0.1689 (mpp) cc_final: -0.2109 (mpp) REVERT: C 102 MET cc_start: 0.4533 (mtm) cc_final: 0.3565 (mtp) REVERT: C 192 MET cc_start: 0.2747 (mmm) cc_final: 0.2411 (mtp) REVERT: C 345 MET cc_start: 0.1394 (ptt) cc_final: 0.0657 (ppp) REVERT: D 174 LEU cc_start: 0.5165 (tp) cc_final: 0.4783 (mp) REVERT: D 277 VAL cc_start: 0.4521 (OUTLIER) cc_final: 0.4314 (m) REVERT: D 345 MET cc_start: 0.6704 (mmt) cc_final: 0.5743 (ptt) outliers start: 43 outliers final: 21 residues processed: 213 average time/residue: 0.1256 time to fit residues: 40.6666 Evaluate side-chains 171 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 175 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 568 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 277 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 158 optimal weight: 0.2980 chunk 169 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 616 HIS ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS B 387 HIS B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.168968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.138932 restraints weight = 43674.209| |-----------------------------------------------------------------------------| r_work (start): 0.4337 rms_B_bonded: 2.97 r_work: 0.4109 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 1.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16464 Z= 0.177 Angle : 0.609 11.079 22310 Z= 0.323 Chirality : 0.040 0.177 2496 Planarity : 0.005 0.074 2822 Dihedral : 4.173 20.928 2174 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 2.32 % Allowed : 15.10 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1978 helix: 1.19 (0.14), residues: 1339 sheet: None (None), residues: 0 loop : -1.62 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 603 TYR 0.046 0.002 TYR A 22 PHE 0.024 0.002 PHE B 460 TRP 0.044 0.002 TRP A 15 HIS 0.009 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00402 (16464) covalent geometry : angle 0.60906 (22310) hydrogen bonds : bond 0.04813 ( 980) hydrogen bonds : angle 4.52642 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.643 Fit side-chains REVERT: A 410 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7053 (mp) REVERT: A 421 LEU cc_start: 0.7595 (tt) cc_final: 0.6591 (mt) REVERT: A 564 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6683 (mp) REVERT: B 74 SER cc_start: 0.5366 (m) cc_final: 0.4906 (p) REVERT: B 308 ARG cc_start: 0.5405 (tpm170) cc_final: 0.4916 (ptp90) REVERT: B 367 TYR cc_start: 0.6100 (m-10) cc_final: 0.5835 (m-10) REVERT: B 398 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: B 468 ARG cc_start: 0.5737 (mmp80) cc_final: 0.4320 (ttm170) REVERT: B 489 MET cc_start: 0.6483 (tpp) cc_final: 0.6272 (ttt) REVERT: B 528 TRP cc_start: 0.7467 (t-100) cc_final: 0.7184 (t-100) REVERT: B 559 TYR cc_start: 0.8292 (m-80) cc_final: 0.8053 (m-80) REVERT: B 617 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8083 (mp) REVERT: C 109 MET cc_start: 0.2658 (ptp) cc_final: 0.1769 (ttm) REVERT: C 345 MET cc_start: 0.2454 (ptt) cc_final: 0.1782 (ppp) REVERT: D 174 LEU cc_start: 0.5338 (tp) cc_final: 0.4669 (mp) REVERT: D 345 MET cc_start: 0.6204 (mmt) cc_final: 0.5104 (ptt) REVERT: D 414 HIS cc_start: 0.5091 (t-90) cc_final: 0.4701 (t-170) outliers start: 40 outliers final: 22 residues processed: 201 average time/residue: 0.1206 time to fit residues: 36.7603 Evaluate side-chains 165 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 271 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 100 optimal weight: 0.0980 chunk 119 optimal weight: 0.0270 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 164 optimal weight: 7.9990 chunk 141 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.169662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.132568 restraints weight = 43402.205| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 3.19 r_work: 0.4062 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 1.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16464 Z= 0.145 Angle : 0.577 10.172 22310 Z= 0.298 Chirality : 0.039 0.146 2496 Planarity : 0.004 0.069 2822 Dihedral : 3.969 16.070 2174 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.55 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 16.78 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 1978 helix: 1.45 (0.14), residues: 1343 sheet: None (None), residues: 0 loop : -1.69 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 217 TYR 0.030 0.002 TYR A 368 PHE 0.023 0.002 PHE B 460 TRP 0.026 0.002 TRP D 176 HIS 0.007 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00324 (16464) covalent geometry : angle 0.57675 (22310) hydrogen bonds : bond 0.04509 ( 980) hydrogen bonds : angle 4.38895 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 TYR cc_start: 0.5959 (m-10) cc_final: 0.5434 (m-10) REVERT: A 138 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5638 (m-80) REVERT: A 181 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5425 (mp0) REVERT: A 408 MET cc_start: 0.7475 (mmp) cc_final: 0.7079 (mmp) REVERT: A 410 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7028 (mp) REVERT: A 421 LEU cc_start: 0.7516 (tt) cc_final: 0.6728 (mm) REVERT: B 398 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: B 468 ARG cc_start: 0.5739 (mmp80) cc_final: 0.5059 (ttm170) REVERT: B 528 TRP cc_start: 0.7662 (t-100) cc_final: 0.7332 (t-100) REVERT: B 559 TYR cc_start: 0.8318 (m-80) cc_final: 0.8095 (m-80) REVERT: B 603 ARG cc_start: 0.7654 (ttp80) cc_final: 0.6836 (ttp80) REVERT: C 43 MET cc_start: -0.1767 (mmp) cc_final: -0.2573 (mpp) REVERT: C 109 MET cc_start: 0.2713 (ptp) cc_final: 0.1060 (ttm) REVERT: C 204 MET cc_start: 0.3318 (ptt) cc_final: 0.2604 (tmm) REVERT: C 345 MET cc_start: 0.1634 (ptt) cc_final: 0.1076 (ppp) REVERT: D 174 LEU cc_start: 0.5080 (tp) cc_final: 0.4595 (mp) REVERT: D 207 LEU cc_start: 0.5431 (tp) cc_final: 0.4982 (mp) REVERT: D 345 MET cc_start: 0.6758 (mmt) cc_final: 0.5551 (ptt) outliers start: 24 outliers final: 12 residues processed: 187 average time/residue: 0.1260 time to fit residues: 36.0466 Evaluate side-chains 162 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 175 TRP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 154 HIS Chi-restraints excluded: chain D residue 171 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 138 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 178 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 187 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.163060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.137592 restraints weight = 41425.249| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 2.68 r_work: 0.4001 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 1.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16464 Z= 0.152 Angle : 0.596 10.967 22310 Z= 0.309 Chirality : 0.039 0.184 2496 Planarity : 0.005 0.081 2822 Dihedral : 3.954 22.581 2174 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 1.39 % Allowed : 17.65 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1978 helix: 1.42 (0.14), residues: 1347 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 16 TYR 0.030 0.002 TYR A 368 PHE 0.025 0.002 PHE B 474 TRP 0.032 0.001 TRP B 15 HIS 0.006 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00340 (16464) covalent geometry : angle 0.59558 (22310) hydrogen bonds : bond 0.04475 ( 980) hydrogen bonds : angle 4.38979 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 30 TYR cc_start: 0.6013 (m-10) cc_final: 0.5807 (m-10) REVERT: A 51 PHE cc_start: 0.6756 (m-10) cc_final: 0.6535 (m-10) REVERT: A 54 PHE cc_start: 0.7283 (t80) cc_final: 0.7052 (t80) REVERT: A 151 LEU cc_start: 0.5979 (pp) cc_final: 0.5768 (mt) REVERT: A 349 LEU cc_start: 0.8372 (mt) cc_final: 0.8169 (mt) REVERT: A 408 MET cc_start: 0.7529 (mmp) cc_final: 0.7118 (mmp) REVERT: A 410 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7033 (mp) REVERT: A 421 LEU cc_start: 0.7755 (tt) cc_final: 0.6942 (mm) REVERT: A 531 LYS cc_start: 0.7254 (ttpt) cc_final: 0.6779 (mmmm) REVERT: B 148 TYR cc_start: 0.7480 (t80) cc_final: 0.7238 (t80) REVERT: B 189 LYS cc_start: 0.7380 (ttpp) cc_final: 0.6828 (tttm) REVERT: B 369 LYS cc_start: 0.8541 (mmmt) cc_final: 0.7724 (pttt) REVERT: B 421 LEU cc_start: 0.6133 (tt) cc_final: 0.5757 (mt) REVERT: B 465 ARG cc_start: 0.5344 (ttt90) cc_final: 0.4730 (tpt-90) REVERT: B 474 PHE cc_start: 0.6818 (t80) cc_final: 0.6570 (t80) REVERT: B 509 VAL cc_start: 0.7964 (m) cc_final: 0.7719 (t) REVERT: B 559 TYR cc_start: 0.8223 (m-80) cc_final: 0.8019 (m-80) REVERT: B 609 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: C 43 MET cc_start: -0.1462 (mmp) cc_final: -0.2457 (mpp) REVERT: C 109 MET cc_start: 0.2732 (ptp) cc_final: 0.1585 (ttp) REVERT: C 204 MET cc_start: 0.3373 (ptt) cc_final: 0.2772 (tmm) REVERT: C 345 MET cc_start: 0.1281 (ptt) cc_final: 0.0842 (ppp) REVERT: D 143 TRP cc_start: 0.1144 (m100) cc_final: 0.0918 (m100) REVERT: D 174 LEU cc_start: 0.5427 (tp) cc_final: 0.4841 (mp) REVERT: D 176 TRP cc_start: 0.0868 (m100) cc_final: 0.0597 (m100) REVERT: D 204 MET cc_start: 0.6398 (mtt) cc_final: 0.6051 (mtp) REVERT: D 207 LEU cc_start: 0.5782 (tp) cc_final: 0.5223 (mp) REVERT: D 345 MET cc_start: 0.6827 (mmt) cc_final: 0.5543 (ptt) outliers start: 24 outliers final: 15 residues processed: 183 average time/residue: 0.1349 time to fit residues: 37.4494 Evaluate side-chains 155 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 339 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 499 HIS Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 154 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 150 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 176 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 0.0470 chunk 163 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 91 optimal weight: 0.0670 chunk 179 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 118 optimal weight: 0.0010 overall best weight: 0.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.167793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.129627 restraints weight = 42662.688| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.25 r_work: 0.4007 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 1.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16464 Z= 0.132 Angle : 0.578 11.838 22310 Z= 0.294 Chirality : 0.038 0.144 2496 Planarity : 0.004 0.042 2822 Dihedral : 3.878 21.609 2174 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 1.39 % Allowed : 17.60 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1978 helix: 1.60 (0.14), residues: 1343 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 502 TYR 0.032 0.002 TYR A 368 PHE 0.024 0.002 PHE B 474 TRP 0.016 0.001 TRP C 143 HIS 0.006 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00293 (16464) covalent geometry : angle 0.57761 (22310) hydrogen bonds : bond 0.04252 ( 980) hydrogen bonds : angle 4.31248 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6368 (mt-10) REVERT: A 181 GLU cc_start: 0.6255 (OUTLIER) cc_final: 0.5987 (mt-10) REVERT: A 408 MET cc_start: 0.7521 (mmp) cc_final: 0.7228 (mmp) REVERT: A 410 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6949 (mp) REVERT: A 421 LEU cc_start: 0.7713 (tt) cc_final: 0.7011 (mm) REVERT: A 531 LYS cc_start: 0.7222 (ttpt) cc_final: 0.6744 (mmmm) REVERT: A 628 ASP cc_start: 0.6450 (t0) cc_final: 0.6226 (t0) REVERT: B 189 LYS cc_start: 0.7532 (ttpp) cc_final: 0.7328 (tttm) REVERT: B 421 LEU cc_start: 0.5984 (tt) cc_final: 0.5671 (mt) REVERT: B 465 ARG cc_start: 0.5572 (ttt90) cc_final: 0.4995 (tpt-90) REVERT: B 474 PHE cc_start: 0.7390 (t80) cc_final: 0.7079 (t80) REVERT: B 528 TRP cc_start: 0.7370 (t-100) cc_final: 0.7037 (t-100) REVERT: B 609 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8117 (m-10) REVERT: C 109 MET cc_start: 0.2867 (ptp) cc_final: 0.1546 (ttp) REVERT: C 204 MET cc_start: 0.3429 (ptt) cc_final: 0.2786 (tmm) REVERT: C 345 MET cc_start: 0.1281 (ptt) cc_final: 0.0849 (ppp) REVERT: D 174 LEU cc_start: 0.5457 (tp) cc_final: 0.4890 (mp) REVERT: D 204 MET cc_start: 0.6540 (mtt) cc_final: 0.6302 (mtp) REVERT: D 241 MET cc_start: 0.6072 (tmm) cc_final: 0.5526 (ttm) REVERT: D 345 MET cc_start: 0.6864 (mmt) cc_final: 0.5656 (ptt) REVERT: D 414 HIS cc_start: 0.5299 (t-90) cc_final: 0.4846 (t-170) outliers start: 24 outliers final: 17 residues processed: 176 average time/residue: 0.1301 time to fit residues: 35.3464 Evaluate side-chains 157 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 609 PHE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 85 HIS Chi-restraints excluded: chain D residue 154 HIS Chi-restraints excluded: chain D residue 264 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 189 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 100 optimal weight: 0.0040 chunk 158 optimal weight: 10.0000 chunk 163 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 71 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 147 ASN ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN C 126 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.167088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.4205 r_free = 0.4205 target = 0.127392 restraints weight = 42560.038| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 2.86 r_work: 0.3954 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 1.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16464 Z= 0.148 Angle : 0.611 11.007 22310 Z= 0.313 Chirality : 0.039 0.253 2496 Planarity : 0.004 0.047 2822 Dihedral : 3.880 19.967 2174 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.41 % Favored : 94.49 % Rotamer: Outliers : 1.16 % Allowed : 18.00 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1978 helix: 1.51 (0.14), residues: 1353 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 225 TYR 0.030 0.002 TYR A 368 PHE 0.022 0.002 PHE A 605 TRP 0.033 0.002 TRP B 528 HIS 0.007 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00336 (16464) covalent geometry : angle 0.61110 (22310) hydrogen bonds : bond 0.04532 ( 980) hydrogen bonds : angle 4.28620 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6738 (mt-10) REVERT: A 94 SER cc_start: 0.6546 (m) cc_final: 0.5939 (p) REVERT: A 408 MET cc_start: 0.7553 (mmp) cc_final: 0.7145 (mmp) REVERT: A 410 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6820 (mp) REVERT: A 421 LEU cc_start: 0.7851 (tt) cc_final: 0.7209 (mm) REVERT: A 531 LYS cc_start: 0.7209 (ttpt) cc_final: 0.6741 (mmmm) REVERT: B 215 MET cc_start: 0.5500 (ppp) cc_final: 0.5287 (tmm) REVERT: B 421 LEU cc_start: 0.6615 (tt) cc_final: 0.6197 (mt) REVERT: B 465 ARG cc_start: 0.5762 (ttt90) cc_final: 0.5141 (tpt-90) REVERT: B 508 MET cc_start: 0.8168 (mmm) cc_final: 0.7961 (mmm) REVERT: B 509 VAL cc_start: 0.8100 (t) cc_final: 0.7803 (p) REVERT: B 528 TRP cc_start: 0.7912 (t-100) cc_final: 0.7431 (t-100) REVERT: C 102 MET cc_start: 0.4887 (mpp) cc_final: 0.3279 (pmm) REVERT: C 109 MET cc_start: 0.2844 (ptp) cc_final: 0.1612 (ttp) REVERT: C 345 MET cc_start: 0.1117 (ptt) cc_final: 0.0824 (ppp) REVERT: D 174 LEU cc_start: 0.5752 (tp) cc_final: 0.5068 (mp) REVERT: D 414 HIS cc_start: 0.5279 (t-90) cc_final: 0.4855 (t-170) outliers start: 20 outliers final: 13 residues processed: 175 average time/residue: 0.1210 time to fit residues: 33.1736 Evaluate side-chains 153 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 415 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 587 HIS Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 154 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 0.0470 chunk 43 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 189 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 ASN D 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.162518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.125136 restraints weight = 40773.818| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.58 r_work: 0.3881 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 1.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16464 Z= 0.170 Angle : 0.621 9.127 22310 Z= 0.321 Chirality : 0.040 0.214 2496 Planarity : 0.004 0.045 2822 Dihedral : 3.997 21.032 2174 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 0.99 % Allowed : 18.82 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1978 helix: 1.41 (0.14), residues: 1339 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 219 TYR 0.031 0.002 TYR A 368 PHE 0.029 0.002 PHE B 460 TRP 0.019 0.002 TRP B 528 HIS 0.006 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00389 (16464) covalent geometry : angle 0.62117 (22310) hydrogen bonds : bond 0.04755 ( 980) hydrogen bonds : angle 4.39372 ( 2940) =============================================================================== Job complete usr+sys time: 4387.61 seconds wall clock time: 75 minutes 52.15 seconds (4552.15 seconds total)