Starting phenix.real_space_refine on Sat Oct 24 09:09:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xj8_66931/10_2026/9xj8_66931.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xj8_66931/10_2026/9xj8_66931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xj8_66931/10_2026/9xj8_66931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xj8_66931/10_2026/9xj8_66931.map" model { file = "/net/cci-nas-00/data/ceres_data/9xj8_66931/10_2026/9xj8_66931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xj8_66931/10_2026/9xj8_66931.cif" } resolution = 4.09 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 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= 0.002 sd= 0.068 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 P 6 5.49 5 S 57 5.16 5 C 8011 2.51 5 N 2155 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12687 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5237 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 15, 'TRANS': 628} Chain breaks: 1 Chain: "B" Number of atoms: 5237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5237 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 15, 'TRANS': 628} Chain breaks: 1 Chain: "E" Number of atoms: 2151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2151 Classifications: {'peptide': 280} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 264} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.21 Number of scatterers: 12687 At special positions: 0 Unit cell: (111.83, 113.94, 144.535, 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) S 57 16.00 P 6 15.00 O 2458 8.00 N 2155 7.00 C 8011 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 513.5 milliseconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 48.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 42 through 66 removed outlier: 4.115A pdb=" N ARG A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.886A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 143 removed outlier: 3.668A pdb=" N TYR A 142 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.610A pdb=" N TYR A 197 " --> pdb=" O GLN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 295 through 299 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 405 through 430 removed outlier: 3.877A pdb=" N LEU A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 452 removed outlier: 3.648A pdb=" N LYS A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 463 removed outlier: 3.891A pdb=" N GLU A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 463 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Processing helix chain 'A' and resid 498 through 504 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 514 Processing helix chain 'A' and resid 524 through 531 removed outlier: 4.436A pdb=" N TYR A 528 " --> pdb=" O PRO A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 580 removed outlier: 5.107A pdb=" N ASN A 570 " --> pdb=" O THR A 566 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU A 571 " --> pdb=" O LYS A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 Processing helix chain 'A' and resid 640 through 653 Processing helix chain 'A' and resid 656 through 675 Processing helix chain 'A' and resid 680 through 696 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 42 through 66 removed outlier: 4.089A pdb=" N ARG B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 removed outlier: 4.196A pdb=" N LEU B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY B 73 " --> pdb=" O LYS B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 113 through 122 removed outlier: 3.780A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.688A pdb=" N TYR B 142 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 199 through 210 removed outlier: 3.566A pdb=" N ILE B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.593A pdb=" N ILE B 304 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 318 Processing helix chain 'B' and resid 379 through 383 Processing helix chain 'B' and resid 405 through 430 removed outlier: 3.648A pdb=" N LEU B 409 " --> pdb=" O GLN B 405 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 452 removed outlier: 3.616A pdb=" N TYR B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 463 removed outlier: 4.459A pdb=" N GLU B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 484 Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 507 through 515 removed outlier: 4.630A pdb=" N LEU B 511 " --> pdb=" O PHE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 removed outlier: 4.178A pdb=" N TYR B 528 " --> pdb=" O PRO B 524 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 533 " --> pdb=" O CYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 580 removed outlier: 5.113A pdb=" N ASN B 570 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU B 571 " --> pdb=" O LYS B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 616 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 640 through 653 Processing helix chain 'B' and resid 656 through 675 removed outlier: 3.502A pdb=" N GLY B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 696 removed outlier: 3.593A pdb=" N HIS B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 160 removed outlier: 3.664A pdb=" N ASP E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 175 through 178 Processing helix chain 'E' and resid 209 through 213 removed outlier: 3.717A pdb=" N LEU E 213 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 235 removed outlier: 3.571A pdb=" N ARG E 235 " --> pdb=" O ALA E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 254 Processing helix chain 'E' and resid 261 through 286 Processing helix chain 'E' and resid 288 through 303 removed outlier: 3.601A pdb=" N HIS E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 320 Processing helix chain 'E' and resid 322 through 337 Proline residue: E 328 - end of helix Processing helix chain 'E' and resid 340 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 174 Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 229 removed outlier: 3.634A pdb=" N ARG A 226 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 331 removed outlier: 3.933A pdb=" N ALA A 325 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 341 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 329 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 389 " --> pdb=" O LYS A 362 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU A 363 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 467 removed outlier: 3.715A pdb=" N TYR A 466 " --> pdb=" O TYR A 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 585 through 588 removed outlier: 6.526A pdb=" N LYS A 585 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE A 636 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 587 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 174 removed outlier: 3.933A pdb=" N LYS B 147 " --> pdb=" O HIS B 189 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 226 through 229 removed outlier: 3.684A pdb=" N ARG B 226 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.864A pdb=" N ALA B 325 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.864A pdb=" N ALA B 325 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU B 363 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 476 removed outlier: 4.257A pdb=" N TYR B 466 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 493 " --> pdb=" O VAL B 542 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 586 through 588 removed outlier: 3.628A pdb=" N ILE B 636 " --> pdb=" O VAL B 587 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 94 through 95 removed outlier: 6.646A pdb=" N THR E 168 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR E 124 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA E 204 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL E 122 " --> pdb=" O ALA E 204 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1797 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: 2.12 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3822 1.34 - 1.46: 1998 1.46 - 1.58: 6972 1.58 - 1.70: 6 1.70 - 1.82: 94 Bond restraints: 12892 Sorted by residual: bond pdb=" CA PRO E 190 " pdb=" C PRO E 190 " ideal model delta sigma weight residual 1.514 1.541 -0.027 5.50e-03 3.31e+04 2.39e+01 bond pdb=" CD2 HIS E 354 " pdb=" NE2 HIS E 354 " ideal model delta sigma weight residual 1.374 1.404 -0.030 1.10e-02 8.26e+03 7.29e+00 bond pdb=" CD2 HIS E 302 " pdb=" NE2 HIS E 302 " ideal model delta sigma weight residual 1.374 1.403 -0.029 1.10e-02 8.26e+03 7.13e+00 bond pdb=" CA PRO E 111 " pdb=" C PRO E 111 " ideal model delta sigma weight residual 1.517 1.542 -0.024 9.30e-03 1.16e+04 6.89e+00 bond pdb=" CZ ARG E 218 " pdb=" NH2 ARG E 218 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.52e+00 ... (remaining 12887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 15950 1.38 - 2.77: 1083 2.77 - 4.15: 293 4.15 - 5.53: 30 5.53 - 6.92: 1 Bond angle restraints: 17357 Sorted by residual: angle pdb=" OE1 GLN E 320 " pdb=" CD GLN E 320 " pdb=" NE2 GLN E 320 " ideal model delta sigma weight residual 122.60 117.27 5.33 1.00e+00 1.00e+00 2.84e+01 angle pdb=" N PRO E 190 " pdb=" CA PRO E 190 " pdb=" CB PRO E 190 " ideal model delta sigma weight residual 103.19 105.87 -2.68 5.60e-01 3.19e+00 2.30e+01 angle pdb=" OE1 GLN E 283 " pdb=" CD GLN E 283 " pdb=" NE2 GLN E 283 " ideal model delta sigma weight residual 122.60 117.84 4.76 1.00e+00 1.00e+00 2.27e+01 angle pdb=" OE1 GLN E 138 " pdb=" CD GLN E 138 " pdb=" NE2 GLN E 138 " ideal model delta sigma weight residual 122.60 118.01 4.59 1.00e+00 1.00e+00 2.11e+01 angle pdb=" C ALA E 326 " pdb=" N ILE E 327 " pdb=" CA ILE E 327 " ideal model delta sigma weight residual 120.33 124.00 -3.67 8.00e-01 1.56e+00 2.11e+01 ... (remaining 17352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 7333 15.07 - 30.14: 538 30.14 - 45.21: 114 45.21 - 60.28: 28 60.28 - 75.35: 10 Dihedral angle restraints: 8023 sinusoidal: 3414 harmonic: 4609 Sorted by residual: dihedral pdb=" CA VAL E 125 " pdb=" C VAL E 125 " pdb=" N HIS E 126 " pdb=" CA HIS E 126 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLU B 353 " pdb=" C GLU B 353 " pdb=" N ASN B 354 " pdb=" CA ASN B 354 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ARG A 620 " pdb=" C ARG A 620 " pdb=" N ASP A 621 " pdb=" CA ASP A 621 " ideal model delta harmonic sigma weight residual -180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1591 0.056 - 0.112: 287 0.112 - 0.168: 63 0.168 - 0.224: 5 0.224 - 0.281: 3 Chirality restraints: 1949 Sorted by residual: chirality pdb=" CB THR E 261 " pdb=" CA THR E 261 " pdb=" OG1 THR E 261 " pdb=" CG2 THR E 261 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ASP E 287 " pdb=" N ASP E 287 " pdb=" C ASP E 287 " pdb=" CB ASP E 287 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ALA E 236 " pdb=" N ALA E 236 " pdb=" C ALA E 236 " pdb=" CB ALA E 236 " both_signs ideal model delta sigma weight residual False 2.48 2.26 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1946 not shown) Planarity restraints: 2211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 179 " -0.076 2.00e-02 2.50e+03 5.44e-02 5.92e+01 pdb=" CG TYR E 179 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR E 179 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR E 179 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR E 179 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR E 179 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR E 179 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 179 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 289 " 0.047 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYR E 289 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR E 289 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR E 289 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR E 289 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR E 289 " -0.034 2.00e-02 2.50e+03 pdb=" CZ TYR E 289 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR E 289 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 177 " -0.039 2.00e-02 2.50e+03 2.61e-02 1.36e+01 pdb=" CG TYR E 177 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR E 177 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 177 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR E 177 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 177 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 177 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR E 177 " -0.049 2.00e-02 2.50e+03 ... (remaining 2208 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 6 2.09 - 2.79: 2608 2.79 - 3.50: 17277 3.50 - 4.20: 28831 4.20 - 4.90: 51457 Nonbonded interactions: 100179 Sorted by model distance: nonbonded pdb=" CA GLY A 695 " pdb=" CD1 LEU E 369 " model vdw 1.388 3.860 nonbonded pdb=" N GLY A 695 " pdb=" CD1 LEU E 369 " model vdw 1.395 3.540 nonbonded pdb=" O GLY B 695 " pdb=" CD1 LEU E 364 " model vdw 1.648 3.460 nonbonded pdb=" CA GLY A 695 " pdb=" CG LEU E 369 " model vdw 1.877 3.870 nonbonded pdb=" CD1 LEU A 694 " pdb=" CD2 TYR E 365 " model vdw 1.910 3.760 ... (remaining 100174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 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 : 0.006 0.318 12893 Z= 0.419 Angle : 0.789 6.918 17357 Z= 0.520 Chirality : 0.048 0.281 1949 Planarity : 0.005 0.076 2211 Dihedral : 11.605 75.347 5035 Min Nonbonded Distance : 1.388 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.25 % Favored : 97.63 % Rotamer: Outliers : 0.07 % Allowed : 0.36 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.25 (0.21), residues: 1558 helix: 1.75 (0.20), residues: 677 sheet: 0.83 (0.34), residues: 254 loop : -0.12 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 136 TYR 0.094 0.003 TYR E 179 PHE 0.029 0.002 PHE E 145 TRP 0.021 0.002 TRP E 93 HIS 0.022 0.002 HIS E 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.31 (12892) covalent geometry : angle 0.78942 / 0.52 (17357) hydrogen bonds : bond 0.17846 / 11.85 ( 634) hydrogen bonds : angle 6.74155 / 4.64 ( 1797) Misc. bond : bond 0.31841 / 16.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7305 (p0) cc_final: 0.6477 (p0) REVERT: A 383 ASN cc_start: 0.8558 (p0) cc_final: 0.8262 (p0) REVERT: A 521 MET cc_start: 0.8594 (mtt) cc_final: 0.8381 (mtt) REVERT: A 532 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8016 (mm-40) REVERT: A 636 ILE cc_start: 0.8843 (pt) cc_final: 0.8639 (pt) REVERT: A 643 ILE cc_start: 0.8136 (mm) cc_final: 0.7750 (mp) REVERT: A 671 LEU cc_start: 0.8938 (mt) cc_final: 0.8698 (mt) REVERT: B 184 THR cc_start: 0.8958 (m) cc_final: 0.8731 (p) REVERT: B 193 ASP cc_start: 0.7705 (p0) cc_final: 0.7468 (t0) REVERT: B 478 LYS cc_start: 0.8719 (tttt) cc_final: 0.8295 (ttmt) REVERT: B 614 MET cc_start: 0.7700 (mmt) cc_final: 0.7325 (mmm) REVERT: B 647 ARG cc_start: 0.6641 (ttp80) cc_final: 0.5364 (tmm160) REVERT: E 337 GLU cc_start: 0.2638 (tt0) cc_final: 0.2211 (tt0) outliers start: 1 outliers final: 0 residues processed: 441 average time/residue: 0.1351 time to fit residues: 81.3032 Evaluate side-chains 206 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 323 HIS A 433 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN B 682 GLN E 126 HIS E 278 ASN ** E 320 GLN ** 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 = 0.4444 r_free = 0.4444 target = 0.206403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.167385 restraints weight = 18316.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.166754 restraints weight = 23775.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.169363 restraints weight = 17618.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.169702 restraints weight = 11569.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.170371 restraints weight = 11198.598| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12893 Z= 0.185 Angle : 0.610 9.576 17357 Z= 0.331 Chirality : 0.043 0.180 1949 Planarity : 0.004 0.047 2211 Dihedral : 5.921 74.802 1761 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.14 (0.21), residues: 1558 helix: 1.72 (0.19), residues: 687 sheet: 0.63 (0.33), residues: 246 loop : -0.20 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 690 TYR 0.021 0.002 TYR A 284 PHE 0.022 0.002 PHE A 20 TRP 0.018 0.002 TRP A 606 HIS 0.009 0.001 HIS B 490 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (12892) covalent geometry : angle 0.60974 / 0.33 (17357) hydrogen bonds : bond 0.04605 / 3.06 ( 634) hydrogen bonds : angle 5.17458 / 3.60 ( 1797) Misc. bond : bond 0.00294 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7018 (p0) cc_final: 0.6171 (p0) REVERT: A 383 ASN cc_start: 0.8784 (p0) cc_final: 0.8436 (p0) REVERT: A 419 LYS cc_start: 0.8237 (tptt) cc_final: 0.7976 (tptt) REVERT: A 549 LEU cc_start: 0.8487 (tt) cc_final: 0.7885 (tt) REVERT: A 591 ARG cc_start: 0.7136 (ptp-170) cc_final: 0.6662 (ptp-170) REVERT: A 669 THR cc_start: 0.8154 (m) cc_final: 0.7828 (m) REVERT: A 671 LEU cc_start: 0.8969 (mt) cc_final: 0.8759 (mt) REVERT: A 691 MET cc_start: 0.7431 (mtp) cc_final: 0.7084 (ttm) REVERT: B 184 THR cc_start: 0.8839 (m) cc_final: 0.8427 (p) REVERT: B 193 ASP cc_start: 0.7507 (p0) cc_final: 0.7290 (t0) REVERT: B 208 LYS cc_start: 0.8475 (tptt) cc_final: 0.8002 (tptm) REVERT: B 463 LEU cc_start: 0.8570 (mt) cc_final: 0.8367 (mt) REVERT: B 574 ILE cc_start: 0.9015 (mt) cc_final: 0.8744 (tp) REVERT: B 647 ARG cc_start: 0.6163 (ttp80) cc_final: 0.5112 (tmm160) REVERT: E 103 ARG cc_start: 0.4549 (ttp80) cc_final: 0.4182 (tmm-80) REVERT: E 357 GLN cc_start: 0.5491 (pt0) cc_final: 0.4517 (pt0) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.1089 time to fit residues: 44.7372 Evaluate side-chains 186 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [130, 80, 97, 134, 119, 146, 148, 73, 18, 26, 121] chunk 130 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 134 optimal weight: 30.0000 chunk 119 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS A 404 GLN B 287 GLN B 291 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN E 278 ASN ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.203269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163904 restraints weight = 18450.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.164259 restraints weight = 22428.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.166609 restraints weight = 16511.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.165783 restraints weight = 11679.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.166096 restraints weight = 11620.670| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12893 Z= 0.206 Angle : 0.613 7.598 17357 Z= 0.333 Chirality : 0.044 0.158 1949 Planarity : 0.004 0.035 2211 Dihedral : 6.261 73.455 1761 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.97 (0.21), residues: 1558 helix: 1.59 (0.20), residues: 689 sheet: 0.46 (0.34), residues: 222 loop : -0.24 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 182 TYR 0.026 0.002 TYR B 381 PHE 0.025 0.002 PHE B 37 TRP 0.012 0.002 TRP A 606 HIS 0.007 0.001 HIS E 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (12892) covalent geometry : angle 0.61273 / 0.33 (17357) hydrogen bonds : bond 0.04370 / 2.88 ( 634) hydrogen bonds : angle 5.07713 / 3.54 ( 1797) Misc. bond : bond 0.00133 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8144 (tpp) cc_final: 0.7471 (ttm) REVERT: A 336 GLU cc_start: 0.7871 (mt-10) cc_final: 0.6965 (tt0) REVERT: A 383 ASN cc_start: 0.9034 (p0) cc_final: 0.8706 (p0) REVERT: A 521 MET cc_start: 0.8357 (mtt) cc_final: 0.7978 (mtt) REVERT: A 557 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: B 193 ASP cc_start: 0.8082 (p0) cc_final: 0.7698 (t0) REVERT: B 208 LYS cc_start: 0.8486 (tptt) cc_final: 0.8029 (tptm) REVERT: B 504 ASN cc_start: 0.7650 (t0) cc_final: 0.7354 (t0) REVERT: B 647 ARG cc_start: 0.6388 (ttp80) cc_final: 0.5383 (tmm160) REVERT: B 674 SER cc_start: 0.9266 (p) cc_final: 0.9040 (p) REVERT: E 103 ARG cc_start: 0.4592 (ttp80) cc_final: 0.4380 (tmm-80) REVERT: E 357 GLN cc_start: 0.5911 (pt0) cc_final: 0.4885 (pt0) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.1028 time to fit residues: 38.9661 Evaluate side-chains 167 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [130, 53, 139, 14, 150, 108, 115, 59, 84, 148, 11] chunk 130 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 139 optimal weight: 0.0870 chunk 14 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 84 optimal weight: 0.0000 chunk 148 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN A 79 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 ASN E 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.200418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.161876 restraints weight = 18815.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.160610 restraints weight = 25380.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.162901 restraints weight = 20343.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.163508 restraints weight = 12958.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163670 restraints weight = 12778.340| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12893 Z= 0.211 Angle : 0.623 7.522 17357 Z= 0.336 Chirality : 0.044 0.236 1949 Planarity : 0.004 0.040 2211 Dihedral : 6.382 80.352 1761 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.30 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.78 (0.21), residues: 1558 helix: 1.50 (0.20), residues: 676 sheet: -0.02 (0.34), residues: 234 loop : -0.24 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 346 TYR 0.026 0.002 TYR B 381 PHE 0.026 0.002 PHE E 238 TRP 0.013 0.002 TRP A 297 HIS 0.008 0.001 HIS E 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (12892) covalent geometry : angle 0.62283 / 0.34 (17357) hydrogen bonds : bond 0.04251 / 2.83 ( 634) hydrogen bonds : angle 5.02178 / 3.50 ( 1797) Misc. bond : bond 0.00517 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8201 (tpp) cc_final: 0.7573 (ttm) REVERT: A 383 ASN cc_start: 0.8996 (p0) cc_final: 0.8628 (p0) REVERT: A 521 MET cc_start: 0.8492 (mtt) cc_final: 0.8279 (mtt) REVERT: A 549 LEU cc_start: 0.8040 (tp) cc_final: 0.7781 (tp) REVERT: A 591 ARG cc_start: 0.7222 (ptp-170) cc_final: 0.6380 (ptp-170) REVERT: B 92 VAL cc_start: 0.6642 (t) cc_final: 0.6436 (t) REVERT: B 208 LYS cc_start: 0.8443 (tptt) cc_final: 0.7952 (tptm) REVERT: B 478 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8103 (mttt) REVERT: B 610 MET cc_start: 0.6705 (tpt) cc_final: 0.6278 (tpt) REVERT: B 647 ARG cc_start: 0.6447 (ttp80) cc_final: 0.6021 (ttp-170) REVERT: B 674 SER cc_start: 0.9306 (p) cc_final: 0.9052 (p) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1037 time to fit residues: 32.8048 Evaluate side-chains 167 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [89, 18, 114, 20, 127, 98, 31, 10, 0, 70, 81] chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.212274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.168893 restraints weight = 20916.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.169816 restraints weight = 16099.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.171733 restraints weight = 11906.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.171854 restraints weight = 8722.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.172541 restraints weight = 8831.808| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12893 Z= 0.128 Angle : 0.540 7.789 17357 Z= 0.293 Chirality : 0.042 0.171 1949 Planarity : 0.003 0.042 2211 Dihedral : 6.258 78.573 1761 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.89 % Favored : 96.98 % Rotamer: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.83 (0.22), residues: 1558 helix: 1.54 (0.20), residues: 681 sheet: -0.06 (0.33), residues: 251 loop : -0.18 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 182 TYR 0.018 0.002 TYR A 438 PHE 0.023 0.002 PHE B 352 TRP 0.016 0.002 TRP E 93 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (12892) covalent geometry : angle 0.53990 / 0.29 (17357) hydrogen bonds : bond 0.03659 / 2.44 ( 634) hydrogen bonds : angle 4.76907 / 3.32 ( 1797) Misc. bond : bond 0.00351 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8030 (tpp) cc_final: 0.7444 (ttm) REVERT: A 336 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6837 (tt0) REVERT: A 383 ASN cc_start: 0.8980 (p0) cc_final: 0.8718 (p0) REVERT: A 521 MET cc_start: 0.8335 (mtt) cc_final: 0.7959 (mtt) REVERT: A 668 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 92 VAL cc_start: 0.6887 (t) cc_final: 0.6664 (t) REVERT: B 208 LYS cc_start: 0.8498 (tptt) cc_final: 0.8018 (tptm) REVERT: B 484 MET cc_start: 0.8310 (ptm) cc_final: 0.8051 (ptt) REVERT: B 504 ASN cc_start: 0.7795 (t0) cc_final: 0.7491 (t0) REVERT: B 666 LEU cc_start: 0.8561 (mt) cc_final: 0.7917 (tt) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1148 time to fit residues: 38.5974 Evaluate side-chains 165 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [145, 94, 101, 69, 45, 126, 72, 48, 12, 100, 124] chunk 145 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 0.0670 chunk 12 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 HIS E 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.213802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.169896 restraints weight = 20774.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.167751 restraints weight = 14576.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.171503 restraints weight = 13165.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.172227 restraints weight = 9617.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.171720 restraints weight = 8647.044| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12893 Z= 0.116 Angle : 0.524 7.861 17357 Z= 0.284 Chirality : 0.041 0.222 1949 Planarity : 0.003 0.038 2211 Dihedral : 6.037 75.905 1761 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.73 % Rotamer: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.92 (0.22), residues: 1558 helix: 1.62 (0.20), residues: 683 sheet: -0.03 (0.32), residues: 261 loop : -0.14 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 182 TYR 0.027 0.002 TYR A 667 PHE 0.025 0.002 PHE E 238 TRP 0.010 0.001 TRP A 162 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (12892) covalent geometry : angle 0.52392 / 0.28 (17357) hydrogen bonds : bond 0.03594 / 2.37 ( 634) hydrogen bonds : angle 4.65477 / 3.25 ( 1797) Misc. bond : bond 0.00199 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.7983 (tpp) cc_final: 0.7379 (ttm) REVERT: A 336 GLU cc_start: 0.7577 (mt-10) cc_final: 0.6838 (tt0) REVERT: A 419 LYS cc_start: 0.8232 (tppt) cc_final: 0.8012 (tptt) REVERT: A 521 MET cc_start: 0.8253 (mtt) cc_final: 0.7777 (mtt) REVERT: A 549 LEU cc_start: 0.8345 (tp) cc_final: 0.7916 (tp) REVERT: A 557 GLU cc_start: 0.8575 (pm20) cc_final: 0.8015 (pm20) REVERT: A 591 ARG cc_start: 0.7085 (ptp-170) cc_final: 0.6264 (ptp-170) REVERT: B 70 LEU cc_start: 0.6952 (tp) cc_final: 0.6722 (mt) REVERT: B 208 LYS cc_start: 0.8455 (tptt) cc_final: 0.8029 (tptm) REVERT: B 484 MET cc_start: 0.8197 (ptm) cc_final: 0.7764 (ptt) REVERT: B 610 MET cc_start: 0.6514 (tpt) cc_final: 0.5842 (tpt) REVERT: B 666 LEU cc_start: 0.8560 (mt) cc_final: 0.7945 (tt) REVERT: B 689 TYR cc_start: 0.7111 (m-80) cc_final: 0.6854 (m-80) REVERT: B 690 ARG cc_start: 0.8212 (ttm110) cc_final: 0.7766 (ttp80) REVERT: E 224 ARG cc_start: 0.3496 (tmt170) cc_final: 0.3061 (tmt170) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1051 time to fit residues: 35.0405 Evaluate side-chains 169 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [103, 146, 27, 28, 98, 43, 13, 56, 123, 94, 20] chunk 103 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 514 HIS ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.212394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.172404 restraints weight = 20808.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173865 restraints weight = 17805.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175296 restraints weight = 13794.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175496 restraints weight = 9881.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.175937 restraints weight = 9744.801| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12893 Z= 0.133 Angle : 0.550 8.192 17357 Z= 0.296 Chirality : 0.041 0.201 1949 Planarity : 0.003 0.040 2211 Dihedral : 6.042 76.084 1761 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.73 % Rotamer: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.94 (0.22), residues: 1558 helix: 1.63 (0.20), residues: 681 sheet: 0.03 (0.33), residues: 261 loop : -0.14 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 386 TYR 0.022 0.002 TYR A 438 PHE 0.016 0.002 PHE B 37 TRP 0.010 0.001 TRP B 162 HIS 0.004 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (12892) covalent geometry : angle 0.54966 / 0.30 (17357) hydrogen bonds : bond 0.03570 / 2.37 ( 634) hydrogen bonds : angle 4.67337 / 3.27 ( 1797) Misc. bond : bond 0.00144 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8072 (tpp) cc_final: 0.7439 (ttm) REVERT: A 297 TRP cc_start: 0.8317 (p90) cc_final: 0.7862 (p90) REVERT: A 336 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6860 (tt0) REVERT: A 383 ASN cc_start: 0.8931 (p0) cc_final: 0.8699 (p0) REVERT: A 419 LYS cc_start: 0.8275 (tppt) cc_final: 0.8034 (tptt) REVERT: A 521 MET cc_start: 0.8319 (mtt) cc_final: 0.7818 (mtt) REVERT: A 668 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 70 LEU cc_start: 0.7156 (tp) cc_final: 0.6921 (mt) REVERT: B 109 THR cc_start: 0.8024 (m) cc_final: 0.7797 (p) REVERT: B 208 LYS cc_start: 0.8403 (tptt) cc_final: 0.8053 (tptm) REVERT: B 484 MET cc_start: 0.8229 (ptm) cc_final: 0.7840 (ptt) REVERT: B 504 ASN cc_start: 0.7747 (t0) cc_final: 0.7410 (t0) REVERT: B 597 CYS cc_start: 0.8370 (p) cc_final: 0.7653 (p) REVERT: B 666 LEU cc_start: 0.8721 (mt) cc_final: 0.8070 (tt) REVERT: B 690 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7751 (ttp80) REVERT: E 164 ASP cc_start: 0.0578 (m-30) cc_final: 0.0267 (m-30) REVERT: E 224 ARG cc_start: 0.3634 (tmt170) cc_final: 0.2998 (tmt170) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1087 time to fit residues: 35.6910 Evaluate side-chains 165 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [18, 71, 79, 21, 52, 134, 147, 106, 99, 135, 8] chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.2980 chunk 134 optimal weight: 7.9990 chunk 147 optimal weight: 50.0000 chunk 106 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 135 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN B 291 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.202577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.162607 restraints weight = 18314.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.161107 restraints weight = 22588.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163498 restraints weight = 17496.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163498 restraints weight = 13210.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.163498 restraints weight = 13210.066| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12893 Z= 0.177 Angle : 0.596 8.702 17357 Z= 0.317 Chirality : 0.043 0.207 1949 Planarity : 0.003 0.043 2211 Dihedral : 6.174 81.227 1761 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 0.07 % Allowed : 1.21 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.88 (0.22), residues: 1558 helix: 1.55 (0.20), residues: 683 sheet: 0.00 (0.32), residues: 261 loop : -0.15 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 483 TYR 0.024 0.002 TYR B 381 PHE 0.017 0.002 PHE B 352 TRP 0.011 0.002 TRP B 162 HIS 0.005 0.001 HIS E 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (12892) covalent geometry : angle 0.59600 / 0.32 (17357) hydrogen bonds : bond 0.03775 / 2.49 ( 634) hydrogen bonds : angle 4.75163 / 3.34 ( 1797) Misc. bond : bond 0.00129 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8111 (tpp) cc_final: 0.7533 (ttm) REVERT: A 213 PHE cc_start: 0.8349 (m-80) cc_final: 0.7862 (m-80) REVERT: A 336 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7038 (tt0) REVERT: A 383 ASN cc_start: 0.9052 (p0) cc_final: 0.8847 (p0) REVERT: A 419 LYS cc_start: 0.8209 (tppt) cc_final: 0.7958 (tptt) REVERT: A 498 THR cc_start: 0.7946 (p) cc_final: 0.6909 (p) REVERT: A 521 MET cc_start: 0.8561 (mtt) cc_final: 0.8112 (mtt) REVERT: A 591 ARG cc_start: 0.7224 (ptp-170) cc_final: 0.7001 (ptp-170) REVERT: A 610 MET cc_start: 0.7140 (tpp) cc_final: 0.6920 (tpp) REVERT: A 668 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7458 (mt-10) REVERT: B 109 THR cc_start: 0.8155 (m) cc_final: 0.7952 (p) REVERT: B 208 LYS cc_start: 0.8373 (tptt) cc_final: 0.7958 (tptm) REVERT: B 484 MET cc_start: 0.8439 (ptm) cc_final: 0.8088 (ptt) REVERT: B 504 ASN cc_start: 0.7812 (t0) cc_final: 0.7471 (t0) REVERT: B 666 LEU cc_start: 0.8658 (mt) cc_final: 0.8138 (tt) REVERT: B 690 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7768 (ttp80) REVERT: E 164 ASP cc_start: 0.0747 (m-30) cc_final: 0.0404 (m-30) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.0982 time to fit residues: 31.5934 Evaluate side-chains 153 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [90, 120, 18, 75, 50, 118, 73, 65, 130, 153, 21] chunk 90 optimal weight: 5.9990 chunk 120 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 130 optimal weight: 50.0000 chunk 153 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN B 444 ASN ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.202905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.164266 restraints weight = 18412.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.163305 restraints weight = 21764.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.165414 restraints weight = 17125.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.165255 restraints weight = 12077.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165877 restraints weight = 11050.990| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12893 Z= 0.165 Angle : 0.598 9.831 17357 Z= 0.321 Chirality : 0.043 0.181 1949 Planarity : 0.003 0.042 2211 Dihedral : 6.238 84.097 1761 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.47 % Rotamer: Outliers : 0.07 % Allowed : 0.71 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.88 (0.22), residues: 1558 helix: 1.50 (0.20), residues: 683 sheet: 0.13 (0.33), residues: 249 loop : -0.14 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 346 TYR 0.027 0.002 TYR A 438 PHE 0.013 0.002 PHE A 20 TRP 0.013 0.002 TRP A 297 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (12892) covalent geometry : angle 0.59807 / 0.32 (17357) hydrogen bonds : bond 0.03823 / 2.52 ( 634) hydrogen bonds : angle 4.74573 / 3.33 ( 1797) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8235 (tpp) cc_final: 0.7577 (ttm) REVERT: A 213 PHE cc_start: 0.7895 (m-80) cc_final: 0.7362 (m-80) REVERT: A 332 GLU cc_start: 0.7105 (mp0) cc_final: 0.6879 (mp0) REVERT: A 336 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6991 (tt0) REVERT: A 521 MET cc_start: 0.8558 (mtt) cc_final: 0.8282 (mtt) REVERT: A 549 LEU cc_start: 0.8057 (tp) cc_final: 0.7807 (tp) REVERT: A 591 ARG cc_start: 0.7245 (ptp-170) cc_final: 0.6365 (ptp-170) REVERT: A 610 MET cc_start: 0.6752 (tpp) cc_final: 0.6530 (tpp) REVERT: A 668 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7156 (mt-10) REVERT: B 208 LYS cc_start: 0.8303 (tptt) cc_final: 0.7798 (tptm) REVERT: B 463 LEU cc_start: 0.8609 (mt) cc_final: 0.8409 (mt) REVERT: B 484 MET cc_start: 0.7973 (ptm) cc_final: 0.7734 (ptt) REVERT: B 625 MET cc_start: 0.5958 (tmm) cc_final: 0.5028 (tmm) REVERT: B 643 ILE cc_start: 0.8018 (mm) cc_final: 0.7813 (mm) REVERT: B 666 LEU cc_start: 0.8707 (mt) cc_final: 0.8286 (tt) REVERT: B 674 SER cc_start: 0.9242 (p) cc_final: 0.8975 (p) REVERT: B 690 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7680 (ttp80) REVERT: E 164 ASP cc_start: 0.0660 (m-30) cc_final: 0.0339 (m-30) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.0907 time to fit residues: 29.7596 Evaluate side-chains 157 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [56, 31, 71, 48, 87, 45, 108, 39, 26, 85, 46] chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 48 optimal weight: 0.0470 chunk 87 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 ASN ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.212345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.173734 restraints weight = 20931.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.169397 restraints weight = 16559.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.170449 restraints weight = 15850.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.171343 restraints weight = 13991.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.171901 restraints weight = 11985.997| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12893 Z= 0.121 Angle : 0.571 9.308 17357 Z= 0.308 Chirality : 0.041 0.179 1949 Planarity : 0.003 0.041 2211 Dihedral : 6.161 81.693 1761 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 0.07 % Allowed : 0.29 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.95 (0.22), residues: 1558 helix: 1.59 (0.20), residues: 681 sheet: 0.19 (0.33), residues: 249 loop : -0.15 (0.26), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.023 0.002 TYR A 284 PHE 0.023 0.002 PHE B 352 TRP 0.012 0.001 TRP A 162 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12892) covalent geometry : angle 0.57087 / 0.31 (17357) hydrogen bonds : bond 0.03521 / 2.32 ( 634) hydrogen bonds : angle 4.62915 / 3.25 ( 1797) Misc. bond : bond 0.00087 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8019 (tpp) cc_final: 0.7453 (ttm) REVERT: A 297 TRP cc_start: 0.8253 (p90) cc_final: 0.7694 (p90) REVERT: A 332 GLU cc_start: 0.7225 (mp0) cc_final: 0.6982 (mp0) REVERT: A 336 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6955 (tt0) REVERT: A 383 ASN cc_start: 0.8853 (p0) cc_final: 0.8641 (p0) REVERT: A 610 MET cc_start: 0.6865 (tpp) cc_final: 0.6603 (tpp) REVERT: A 668 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 98 MET cc_start: 0.8116 (mpp) cc_final: 0.7632 (mpp) REVERT: B 208 LYS cc_start: 0.8257 (tptt) cc_final: 0.7766 (tptm) REVERT: B 213 PHE cc_start: 0.8258 (m-80) cc_final: 0.7764 (m-80) REVERT: B 352 PHE cc_start: 0.7497 (m-80) cc_final: 0.7083 (m-80) REVERT: B 484 MET cc_start: 0.8302 (ptm) cc_final: 0.8004 (ptt) REVERT: B 588 VAL cc_start: 0.8898 (t) cc_final: 0.8243 (t) REVERT: B 625 MET cc_start: 0.5990 (tmm) cc_final: 0.5150 (tmm) REVERT: B 666 LEU cc_start: 0.8560 (mt) cc_final: 0.7867 (tt) REVERT: B 690 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7763 (ttp80) REVERT: E 164 ASP cc_start: 0.0738 (m-30) cc_final: 0.0457 (m-30) REVERT: E 170 MET cc_start: 0.1194 (mtp) cc_final: 0.0176 (ppp) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.0972 time to fit residues: 31.5622 Evaluate side-chains 158 residues out of total 1403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: [15, 18, 117, 22, 130, 123, 77, 19, 124, 116, 24] chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 22 optimal weight: 0.0020 chunk 130 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 194 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN B 291 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 HIS ** E 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.211859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.172595 restraints weight = 21073.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170961 restraints weight = 20567.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.172548 restraints weight = 18775.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.173671 restraints weight = 14567.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.174015 restraints weight = 11493.966| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12893 Z= 0.126 Angle : 0.594 14.627 17357 Z= 0.319 Chirality : 0.042 0.192 1949 Planarity : 0.004 0.049 2211 Dihedral : 6.107 81.227 1761 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.66 % Rotamer: Outliers : 0.07 % Allowed : 0.71 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.90 (0.22), residues: 1558 helix: 1.50 (0.20), residues: 683 sheet: 0.26 (0.33), residues: 253 loop : -0.17 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 346 TYR 0.019 0.002 TYR A 284 PHE 0.017 0.002 PHE B 37 TRP 0.015 0.001 TRP A 297 HIS 0.005 0.001 HIS B 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (12892) covalent geometry : angle 0.59409 / 0.32 (17357) hydrogen bonds : bond 0.03551 / 2.33 ( 634) hydrogen bonds : angle 4.63772 / 3.26 ( 1797) Misc. bond : bond 0.00642 / 0.34 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.46 seconds wall clock time: 35 minutes 1.14 seconds (2101.14 seconds total)