Starting phenix.real_space_refine on Thu Aug 6 17:28:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxf_37905/08_2026/8wxf_37905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxf_37905/08_2026/8wxf_37905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2026/8wxf_37905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2026/8wxf_37905.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2026/8wxf_37905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxf_37905/08_2026/8wxf_37905.cif" } resolution = 4.0 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 10302 2.51 5 N 2820 2.21 5 O 3210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16380 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "B" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Chain: "C" Number of atoms: 5460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5460 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 35, 'TRANS': 694} Time building chain proxies: 3.57, per 1000 atoms: 0.22 Number of scatterers: 16380 At special positions: 0 Unit cell: (116.16, 113.52, 146.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 3210 8.00 N 2820 7.00 C 10302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 667.2 milliseconds 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3966 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 21 sheets defined 34.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.645A pdb=" N ALA A 81 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 82 " --> pdb=" O MET A 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 78 through 82' Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 139 through 153 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.099A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 283 through 293 removed outlier: 4.055A pdb=" N ALA A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.500A pdb=" N GLY A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.220A pdb=" N THR A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'A' and resid 561 through 584 Processing helix chain 'A' and resid 606 through 611 Processing helix chain 'A' and resid 617 through 626 Processing helix chain 'A' and resid 643 through 658 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.917A pdb=" N ALA B 82 " --> pdb=" O MET B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 178 through 185 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 225 through 254 Proline residue: B 238 - end of helix removed outlier: 3.673A pdb=" N ALA B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 Processing helix chain 'B' and resid 283 through 292 removed outlier: 4.024A pdb=" N ALA B 287 " --> pdb=" O THR B 283 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 314 Processing helix chain 'B' and resid 321 through 343 Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'B' and resid 469 through 485 removed outlier: 3.540A pdb=" N GLY B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 561 through 584 Processing helix chain 'B' and resid 606 through 611 removed outlier: 4.488A pdb=" N VAL B 610 " --> pdb=" O LYS B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 643 through 659 removed outlier: 3.753A pdb=" N ASN B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.617A pdb=" N ALA C 81 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 82 " --> pdb=" O MET C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 139 through 153 Processing helix chain 'C' and resid 178 through 185 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 225 through 254 Proline residue: C 238 - end of helix Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.528A pdb=" N ILE C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 4.041A pdb=" N ASP C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 344 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.640A pdb=" N THR C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.550A pdb=" N ILE C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 removed outlier: 3.646A pdb=" N GLY C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 561 through 584 Processing helix chain 'C' and resid 603 through 611 removed outlier: 3.539A pdb=" N ILE C 607 " --> pdb=" O PRO C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 626 Processing helix chain 'C' and resid 643 through 658 Processing helix chain 'C' and resid 694 through 699 removed outlier: 4.555A pdb=" N GLY C 699 " --> pdb=" O ILE C 695 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.777A pdb=" N ILE A 17 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG A 25 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 52 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N MET A 51 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 124 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 125 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 173 removed outlier: 6.615A pdb=" N VAL A 190 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 205 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 192 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.921A pdb=" N GLN A 380 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 457 " --> pdb=" O THR A 386 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET A 408 " --> pdb=" O GLN A 458 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 460 " --> pdb=" O MET A 408 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 410 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA A 462 " --> pdb=" O HIS A 410 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 493 through 494 removed outlier: 6.800A pdb=" N ALA A 539 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 498 through 499 removed outlier: 3.869A pdb=" N LEU A 499 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 597 Processing sheet with id=AA8, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.344A pdb=" N MET B 51 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 124 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 125 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 172 through 175 removed outlier: 3.997A pdb=" N PHE B 187 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 190 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL B 205 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 192 " --> pdb=" O MET B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 381 through 388 removed outlier: 6.721A pdb=" N MET B 408 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER B 460 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 498 through 499 Processing sheet with id=AB4, first strand: chain 'B' and resid 539 through 540 removed outlier: 6.834A pdb=" N ALA B 539 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG C 25 " --> pdb=" O ILE C 17 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 17 " --> pdb=" O ARG C 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 7 removed outlier: 5.739A pdb=" N GLU C 5 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLU C 12 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 7 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU C 30 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 52 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET C 51 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 124 " --> pdb=" O THR C 57 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE C 125 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 172 through 175 removed outlier: 6.718A pdb=" N VAL C 190 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL C 205 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA C 192 " --> pdb=" O MET C 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 380 through 388 removed outlier: 6.174A pdb=" N GLN C 380 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 408 " --> pdb=" O GLN C 458 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N SER C 460 " --> pdb=" O MET C 408 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 498 through 500 removed outlier: 3.764A pdb=" N VAL C 519 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 539 through 540 removed outlier: 6.870A pdb=" N ALA C 539 " --> pdb=" O THR C 546 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 631 removed outlier: 3.633A pdb=" N PHE C 638 " --> pdb=" O SER C 630 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 723 through 724 removed outlier: 4.114A pdb=" N ASP C 723 " --> pdb=" O SER C 731 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 731 " --> pdb=" O ASP C 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 657 hydrogen bonds defined for protein. 1878 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: 2.74 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5634 1.34 - 1.46: 3225 1.46 - 1.58: 7680 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 16626 Sorted by residual: bond pdb=" N VAL B 278 " pdb=" CA VAL B 278 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.19e+00 bond pdb=" N GLU C 77 " pdb=" CA GLU C 77 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.52e+00 bond pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.23e-02 6.61e+03 6.52e+00 bond pdb=" N LEU C 313 " pdb=" CA LEU C 313 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.33e-02 5.65e+03 6.17e+00 bond pdb=" N MET C 497 " pdb=" CA MET C 497 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.07e+00 ... (remaining 16621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 22045 2.05 - 4.10: 436 4.10 - 6.15: 64 6.15 - 8.20: 14 8.20 - 10.25: 7 Bond angle restraints: 22566 Sorted by residual: angle pdb=" N VAL C 186 " pdb=" CA VAL C 186 " pdb=" C VAL C 186 " ideal model delta sigma weight residual 113.47 108.80 4.67 1.01e+00 9.80e-01 2.14e+01 angle pdb=" N VAL A 510 " pdb=" CA VAL A 510 " pdb=" C VAL A 510 " ideal model delta sigma weight residual 113.71 109.59 4.12 9.50e-01 1.11e+00 1.88e+01 angle pdb=" N ASP C 47 " pdb=" CA ASP C 47 " pdb=" C ASP C 47 " ideal model delta sigma weight residual 112.86 107.89 4.97 1.22e+00 6.72e-01 1.66e+01 angle pdb=" CA GLU A 515 " pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLN A 311 " pdb=" CB GLN A 311 " pdb=" CG GLN A 311 " ideal model delta sigma weight residual 114.10 121.49 -7.39 2.00e+00 2.50e-01 1.37e+01 ... (remaining 22561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 8590 17.48 - 34.97: 1139 34.97 - 52.45: 290 52.45 - 69.93: 51 69.93 - 87.42: 34 Dihedral angle restraints: 10104 sinusoidal: 3918 harmonic: 6186 Sorted by residual: dihedral pdb=" CA GLU B 515 " pdb=" C GLU B 515 " pdb=" N ARG B 516 " pdb=" CA ARG B 516 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU A 554 " pdb=" C LEU A 554 " pdb=" N ASP A 555 " pdb=" CA ASP A 555 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 524 " pdb=" C ILE B 524 " pdb=" N LEU B 525 " pdb=" CA LEU B 525 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1995 0.047 - 0.095: 502 0.095 - 0.142: 169 0.142 - 0.189: 8 0.189 - 0.236: 2 Chirality restraints: 2676 Sorted by residual: chirality pdb=" CB VAL B 561 " pdb=" CA VAL B 561 " pdb=" CG1 VAL B 561 " pdb=" CG2 VAL B 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL A 561 " pdb=" CA VAL A 561 " pdb=" CG1 VAL A 561 " pdb=" CG2 VAL A 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA VAL B 278 " pdb=" N VAL B 278 " pdb=" C VAL B 278 " pdb=" CB VAL B 278 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 2673 not shown) Planarity restraints: 2979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 557 " 0.058 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO B 558 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 558 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 558 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 267 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO B 268 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 47 " 0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" CG ASP B 47 " -0.055 2.00e-02 2.50e+03 pdb=" OD1 ASP B 47 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP B 47 " 0.019 2.00e-02 2.50e+03 ... (remaining 2976 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1107 2.73 - 3.27: 17011 3.27 - 3.82: 25895 3.82 - 4.36: 28346 4.36 - 4.90: 48783 Nonbonded interactions: 121142 Sorted by model distance: nonbonded pdb=" O ASP A 343 " pdb=" ND1 HIS A 344 " model vdw 2.188 3.120 nonbonded pdb=" O ASN A 655 " pdb=" NE2 GLN A 661 " model vdw 2.224 3.120 nonbonded pdb=" O ALA B 287 " pdb=" OG1 THR B 291 " model vdw 2.236 3.040 nonbonded pdb=" NH1 ARG C 356 " pdb=" OD2 ASP C 523 " model vdw 2.239 3.120 nonbonded pdb=" NH1 ARG C 350 " pdb=" O GLY C 351 " model vdw 2.243 3.120 ... (remaining 121137 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.260 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16626 Z= 0.164 Angle : 0.709 10.247 22566 Z= 0.386 Chirality : 0.046 0.236 2676 Planarity : 0.005 0.087 2979 Dihedral : 17.293 87.415 6138 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 0.75 % Allowed : 33.16 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.18), residues: 2184 helix: 0.61 (0.20), residues: 693 sheet: -1.44 (0.31), residues: 325 loop : -1.55 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 406 TYR 0.010 0.001 TYR B 276 PHE 0.014 0.001 PHE C 531 TRP 0.003 0.001 TRP A 173 HIS 0.003 0.001 HIS B 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (16626) covalent geometry : angle 0.70893 / 0.39 (22566) hydrogen bonds : bond 0.17475 / 11.42 ( 654) hydrogen bonds : angle 6.96870 / 4.76 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASP cc_start: 0.9054 (m-30) cc_final: 0.8764 (p0) REVERT: A 333 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8944 (tttt) REVERT: A 337 ARG cc_start: 0.9115 (mtp85) cc_final: 0.8662 (mtp85) REVERT: B 328 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9277 (mt) REVERT: C 208 GLU cc_start: 0.6663 (tp30) cc_final: 0.6335 (tp30) REVERT: C 249 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8224 (mt-10) REVERT: C 482 LEU cc_start: 0.8746 (mm) cc_final: 0.8314 (mm) REVERT: C 495 ILE cc_start: 0.8604 (mp) cc_final: 0.8190 (mm) REVERT: C 534 MET cc_start: 0.7696 (tpt) cc_final: 0.7452 (tpp) outliers start: 13 outliers final: 4 residues processed: 199 average time/residue: 0.1115 time to fit residues: 35.3473 Evaluate side-chains 184 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 179 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.0980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106183 restraints weight = 31512.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104953 restraints weight = 22400.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106176 restraints weight = 17939.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106564 restraints weight = 14975.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106871 restraints weight = 13001.176| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16626 Z= 0.168 Angle : 0.618 9.700 22566 Z= 0.320 Chirality : 0.045 0.216 2676 Planarity : 0.005 0.059 2979 Dihedral : 4.785 55.781 2357 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.14 % Rotamer: Outliers : 5.07 % Allowed : 28.09 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2184 helix: 0.84 (0.20), residues: 699 sheet: -1.31 (0.30), residues: 329 loop : -1.43 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 350 TYR 0.012 0.002 TYR B 270 PHE 0.018 0.001 PHE A 531 TRP 0.006 0.001 TRP C 173 HIS 0.002 0.001 HIS B 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16626) covalent geometry : angle 0.61778 / 0.32 (22566) hydrogen bonds : bond 0.04005 / 2.70 ( 654) hydrogen bonds : angle 5.39692 / 3.71 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 182 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7617 (tp30) cc_final: 0.7408 (tp30) REVERT: A 345 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8547 (p90) REVERT: A 442 LEU cc_start: 0.8805 (tp) cc_final: 0.8587 (tp) REVERT: A 482 LEU cc_start: 0.9102 (mm) cc_final: 0.8636 (mm) REVERT: A 522 THR cc_start: 0.9305 (m) cc_final: 0.8819 (p) REVERT: B 389 MET cc_start: 0.8186 (mmm) cc_final: 0.7977 (mtt) REVERT: C 50 ASN cc_start: 0.8489 (m-40) cc_final: 0.8252 (m-40) REVERT: C 215 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8651 (pp20) REVERT: C 482 LEU cc_start: 0.8750 (mm) cc_final: 0.8234 (mm) outliers start: 88 outliers final: 48 residues processed: 248 average time/residue: 0.0983 time to fit residues: 39.6474 Evaluate side-chains 211 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 145 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 HIS B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 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 = 0.3925 r_free = 0.3925 target = 0.147029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101197 restraints weight = 31268.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104148 restraints weight = 18011.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106142 restraints weight = 12604.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107368 restraints weight = 10045.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.108199 restraints weight = 8762.958| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16626 Z= 0.168 Angle : 0.599 11.551 22566 Z= 0.307 Chirality : 0.044 0.204 2676 Planarity : 0.005 0.057 2979 Dihedral : 4.546 54.153 2355 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 5.31 % Allowed : 28.09 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.18), residues: 2184 helix: 0.98 (0.20), residues: 702 sheet: -1.32 (0.29), residues: 329 loop : -1.34 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 406 TYR 0.019 0.002 TYR A 276 PHE 0.022 0.001 PHE B 345 TRP 0.006 0.001 TRP C 173 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16626) covalent geometry : angle 0.59940 / 0.31 (22566) hydrogen bonds : bond 0.03885 / 2.63 ( 654) hydrogen bonds : angle 5.12465 / 3.53 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 165 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.8798 (tp) cc_final: 0.8578 (tp) REVERT: A 522 THR cc_start: 0.9226 (m) cc_final: 0.8743 (p) REVERT: B 389 MET cc_start: 0.8231 (mmm) cc_final: 0.8014 (mtt) REVERT: C 30 GLU cc_start: 0.8172 (tt0) cc_final: 0.7740 (mt-10) REVERT: C 215 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8712 (pp20) REVERT: C 249 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 320 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7206 (mtm-85) REVERT: C 497 MET cc_start: 0.8137 (mmt) cc_final: 0.7911 (mmm) outliers start: 92 outliers final: 56 residues processed: 233 average time/residue: 0.1068 time to fit residues: 40.5559 Evaluate side-chains 223 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 545 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 94 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 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 = 0.3896 r_free = 0.3896 target = 0.144695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102835 restraints weight = 31611.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101589 restraints weight = 22860.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102112 restraints weight = 19129.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102712 restraints weight = 16087.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103037 restraints weight = 13846.011| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16626 Z= 0.237 Angle : 0.647 11.992 22566 Z= 0.331 Chirality : 0.046 0.325 2676 Planarity : 0.005 0.059 2979 Dihedral : 4.704 54.778 2355 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.46 % Favored : 93.41 % Rotamer: Outliers : 6.29 % Allowed : 28.09 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.18), residues: 2184 helix: 0.90 (0.20), residues: 708 sheet: -1.36 (0.29), residues: 312 loop : -1.41 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 339 TYR 0.015 0.002 TYR A 80 PHE 0.027 0.002 PHE A 345 TRP 0.004 0.001 TRP C 173 HIS 0.004 0.001 HIS C 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (16626) covalent geometry : angle 0.64658 / 0.33 (22566) hydrogen bonds : bond 0.04035 / 2.75 ( 654) hydrogen bonds : angle 5.13520 / 3.54 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 161 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8576 (m) REVERT: A 311 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8973 (mm-40) REVERT: A 695 ILE cc_start: 0.1860 (OUTLIER) cc_final: 0.1610 (pt) REVERT: B 412 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8377 (m-40) REVERT: C 30 GLU cc_start: 0.8153 (tt0) cc_final: 0.7755 (mt-10) REVERT: C 50 ASN cc_start: 0.8568 (m-40) cc_final: 0.8263 (m-40) REVERT: C 215 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8734 (pp20) REVERT: C 320 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7151 (mtm-85) REVERT: C 497 MET cc_start: 0.8112 (mmt) cc_final: 0.7827 (mmm) outliers start: 109 outliers final: 75 residues processed: 247 average time/residue: 0.1030 time to fit residues: 41.6583 Evaluate side-chains 235 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 155 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 392 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 58 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.9278 > 50:) chunk 140 optimal weight: 20.0000 chunk 141 optimal weight: 0.3980 chunk 213 optimal weight: 0.0980 chunk 19 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 143 optimal weight: 0.0870 chunk 192 optimal weight: 0.3980 chunk 155 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN B 308 GLN B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 458 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 = 0.3942 r_free = 0.3942 target = 0.148359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107333 restraints weight = 30691.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107291 restraints weight = 20790.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108180 restraints weight = 16441.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108997 restraints weight = 13657.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108984 restraints weight = 11706.909| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16626 Z= 0.112 Angle : 0.583 14.538 22566 Z= 0.290 Chirality : 0.044 0.247 2676 Planarity : 0.004 0.054 2979 Dihedral : 4.417 54.242 2355 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 4.50 % Allowed : 29.64 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.73 (0.18), residues: 2184 helix: 1.00 (0.20), residues: 705 sheet: -1.21 (0.29), residues: 328 loop : -1.21 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 329 TYR 0.010 0.001 TYR C 80 PHE 0.022 0.001 PHE A 531 TRP 0.003 0.001 TRP B 173 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (16626) covalent geometry : angle 0.58268 / 0.29 (22566) hydrogen bonds : bond 0.03294 / 2.24 ( 654) hydrogen bonds : angle 4.84676 / 3.34 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 GLN cc_start: 0.9241 (mm-40) cc_final: 0.9006 (mm-40) REVERT: A 442 LEU cc_start: 0.8816 (tp) cc_final: 0.8590 (tp) REVERT: C 30 GLU cc_start: 0.8195 (tt0) cc_final: 0.7711 (mt-10) REVERT: C 215 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8733 (pp20) REVERT: C 249 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 320 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6819 (mtm180) REVERT: C 497 MET cc_start: 0.8105 (mmt) cc_final: 0.7839 (mmm) outliers start: 78 outliers final: 57 residues processed: 240 average time/residue: 0.1039 time to fit residues: 40.7434 Evaluate side-chains 227 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 31 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.0020 chunk 136 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 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 = 0.3923 r_free = 0.3923 target = 0.146852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105527 restraints weight = 31478.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104258 restraints weight = 22173.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105225 restraints weight = 18451.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105808 restraints weight = 14663.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106207 restraints weight = 13167.890| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16626 Z= 0.156 Angle : 0.606 13.145 22566 Z= 0.300 Chirality : 0.044 0.301 2676 Planarity : 0.005 0.054 2979 Dihedral : 4.262 53.400 2352 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.22 % Favored : 94.64 % Rotamer: Outliers : 4.90 % Allowed : 29.99 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2184 helix: 1.04 (0.20), residues: 706 sheet: -1.26 (0.29), residues: 327 loop : -1.19 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.010 0.001 TYR A 80 PHE 0.022 0.001 PHE A 531 TRP 0.004 0.001 TRP B 173 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (16626) covalent geometry : angle 0.60561 / 0.30 (22566) hydrogen bonds : bond 0.03457 / 2.36 ( 654) hydrogen bonds : angle 4.84727 / 3.34 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 164 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.8771 (tp) cc_final: 0.8520 (tp) REVERT: A 555 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7809 (t0) REVERT: A 695 ILE cc_start: 0.1572 (OUTLIER) cc_final: 0.1347 (pt) REVERT: B 548 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8711 (mp) REVERT: C 30 GLU cc_start: 0.8164 (tt0) cc_final: 0.7734 (mt-10) REVERT: C 50 ASN cc_start: 0.8471 (m-40) cc_final: 0.8187 (m-40) REVERT: C 215 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8769 (pp20) REVERT: C 320 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7132 (mtm-85) REVERT: C 497 MET cc_start: 0.8193 (mmt) cc_final: 0.7844 (mmm) outliers start: 85 outliers final: 71 residues processed: 233 average time/residue: 0.1016 time to fit residues: 39.0821 Evaluate side-chains 234 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 158 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 171 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 83 optimal weight: 0.0010 chunk 27 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100147 restraints weight = 31007.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103026 restraints weight = 17875.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.104974 restraints weight = 12550.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106216 restraints weight = 10024.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106843 restraints weight = 8729.950| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16626 Z= 0.169 Angle : 0.614 12.890 22566 Z= 0.305 Chirality : 0.045 0.306 2676 Planarity : 0.005 0.054 2979 Dihedral : 4.327 52.884 2352 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 5.77 % Allowed : 29.12 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2184 helix: 1.07 (0.20), residues: 707 sheet: -1.39 (0.28), residues: 338 loop : -1.20 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.010 0.002 TYR A 411 PHE 0.022 0.001 PHE A 531 TRP 0.003 0.001 TRP B 173 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (16626) covalent geometry : angle 0.61389 / 0.30 (22566) hydrogen bonds : bond 0.03536 / 2.43 ( 654) hydrogen bonds : angle 4.82349 / 3.33 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 163 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 ASP cc_start: 0.8968 (m-30) cc_final: 0.8744 (p0) REVERT: A 318 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: A 442 LEU cc_start: 0.8771 (tp) cc_final: 0.8518 (tp) REVERT: A 555 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.7839 (t0) REVERT: B 51 MET cc_start: 0.8460 (ttt) cc_final: 0.8220 (ttt) REVERT: B 548 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8578 (mp) REVERT: B 693 VAL cc_start: 0.4544 (OUTLIER) cc_final: 0.4273 (t) REVERT: C 30 GLU cc_start: 0.8201 (tt0) cc_final: 0.7659 (mt-10) REVERT: C 50 ASN cc_start: 0.8613 (m-40) cc_final: 0.8293 (m-40) REVERT: C 79 MET cc_start: 0.8669 (mmm) cc_final: 0.8281 (tpp) REVERT: C 215 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8771 (pp20) REVERT: C 320 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7183 (mtm-85) outliers start: 100 outliers final: 78 residues processed: 246 average time/residue: 0.1036 time to fit residues: 41.6173 Evaluate side-chains 240 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 156 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 13 optimal weight: 0.0570 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 chunk 99 optimal weight: 0.0030 overall best weight: 0.5308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.148429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103322 restraints weight = 30781.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106359 restraints weight = 17596.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108353 restraints weight = 12215.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109619 restraints weight = 9720.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.110341 restraints weight = 8457.670| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16626 Z= 0.110 Angle : 0.597 12.356 22566 Z= 0.292 Chirality : 0.044 0.209 2676 Planarity : 0.005 0.053 2979 Dihedral : 4.151 51.825 2352 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.35 % Favored : 95.51 % Rotamer: Outliers : 4.44 % Allowed : 30.57 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2184 helix: 1.09 (0.20), residues: 706 sheet: -1.20 (0.29), residues: 336 loop : -1.10 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 516 TYR 0.008 0.001 TYR C 276 PHE 0.022 0.001 PHE A 531 TRP 0.002 0.001 TRP C 173 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (16626) covalent geometry : angle 0.59678 / 0.29 (22566) hydrogen bonds : bond 0.03102 / 2.11 ( 654) hydrogen bonds : angle 4.67892 / 3.23 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 184 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: A 208 GLU cc_start: 0.7373 (tp30) cc_final: 0.7113 (tp30) REVERT: A 249 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8055 (mt-10) REVERT: A 318 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: A 555 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7747 (t0) REVERT: A 695 ILE cc_start: 0.1439 (OUTLIER) cc_final: 0.1223 (pt) REVERT: B 208 GLU cc_start: 0.7553 (tp30) cc_final: 0.7025 (tp30) REVERT: B 548 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8521 (mp) REVERT: B 590 MET cc_start: 0.5903 (tpp) cc_final: 0.5663 (tpp) REVERT: B 693 VAL cc_start: 0.4533 (OUTLIER) cc_final: 0.4275 (t) REVERT: C 30 GLU cc_start: 0.8210 (tt0) cc_final: 0.7632 (mt-10) REVERT: C 50 ASN cc_start: 0.8529 (m-40) cc_final: 0.8197 (m-40) REVERT: C 79 MET cc_start: 0.8651 (mmm) cc_final: 0.8250 (tpp) REVERT: C 215 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8749 (pp20) REVERT: C 320 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6878 (mtm-85) REVERT: C 431 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7469 (tm-30) REVERT: C 497 MET cc_start: 0.7833 (mmt) cc_final: 0.7436 (mmm) outliers start: 77 outliers final: 62 residues processed: 245 average time/residue: 0.1026 time to fit residues: 41.3426 Evaluate side-chains 244 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 174 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 6 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 106 optimal weight: 9.9990 chunk 201 optimal weight: 0.0370 chunk 180 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.1064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 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 = 0.3910 r_free = 0.3910 target = 0.145924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105865 restraints weight = 31153.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103934 restraints weight = 23648.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105001 restraints weight = 18881.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105565 restraints weight = 14877.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.105836 restraints weight = 13298.330| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16626 Z= 0.184 Angle : 0.643 14.145 22566 Z= 0.317 Chirality : 0.045 0.304 2676 Planarity : 0.005 0.054 2979 Dihedral : 4.164 50.890 2351 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.40 % Favored : 94.46 % Rotamer: Outliers : 4.84 % Allowed : 30.74 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2184 helix: 1.10 (0.20), residues: 707 sheet: -1.34 (0.28), residues: 338 loop : -1.13 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 516 TYR 0.013 0.002 TYR A 80 PHE 0.022 0.001 PHE A 531 TRP 0.003 0.001 TRP C 173 HIS 0.005 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (16626) covalent geometry : angle 0.64282 / 0.32 (22566) hydrogen bonds : bond 0.03482 / 2.38 ( 654) hydrogen bonds : angle 4.78385 / 3.30 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 171 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: A 555 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 695 ILE cc_start: 0.1622 (OUTLIER) cc_final: 0.1369 (pt) REVERT: B 51 MET cc_start: 0.8272 (ttt) cc_final: 0.8053 (ttt) REVERT: B 548 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8715 (mp) REVERT: B 562 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8758 (tt) REVERT: B 693 VAL cc_start: 0.4712 (OUTLIER) cc_final: 0.4447 (t) REVERT: C 30 GLU cc_start: 0.8190 (tt0) cc_final: 0.7733 (mt-10) REVERT: C 50 ASN cc_start: 0.8527 (m-40) cc_final: 0.8191 (m-40) REVERT: C 79 MET cc_start: 0.8619 (mmm) cc_final: 0.8187 (tpp) REVERT: C 215 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8763 (pp20) REVERT: C 313 LEU cc_start: 0.8669 (mp) cc_final: 0.8069 (tt) REVERT: C 320 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7019 (mtm180) REVERT: C 497 MET cc_start: 0.7973 (mmt) cc_final: 0.7669 (mmm) outliers start: 84 outliers final: 67 residues processed: 235 average time/residue: 0.1004 time to fit residues: 38.9765 Evaluate side-chains 241 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 166 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 392 MET Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 42 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 139 optimal weight: 0.0570 chunk 102 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 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 = 0.3947 r_free = 0.3947 target = 0.148659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.108126 restraints weight = 30634.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.108162 restraints weight = 20068.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.109133 restraints weight = 15410.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.109882 restraints weight = 12926.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110081 restraints weight = 11592.618| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16626 Z= 0.113 Angle : 0.621 15.020 22566 Z= 0.301 Chirality : 0.045 0.255 2676 Planarity : 0.004 0.054 2979 Dihedral : 4.066 50.410 2351 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.26 % Favored : 95.60 % Rotamer: Outliers : 4.04 % Allowed : 31.37 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.18), residues: 2184 helix: 1.08 (0.20), residues: 707 sheet: -1.20 (0.28), residues: 338 loop : -1.04 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 516 TYR 0.014 0.001 TYR B 276 PHE 0.022 0.001 PHE A 531 TRP 0.002 0.001 TRP C 173 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (16626) covalent geometry : angle 0.62079 / 0.30 (22566) hydrogen bonds : bond 0.03108 / 2.12 ( 654) hydrogen bonds : angle 4.66192 / 3.21 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4368 Ramachandran restraints generated. 2184 Oldfield, 0 Emsley, 2184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 555 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7731 (t0) REVERT: B 204 MET cc_start: 0.8895 (tmm) cc_final: 0.8655 (tpt) REVERT: B 208 GLU cc_start: 0.7600 (tp30) cc_final: 0.7088 (tp30) REVERT: B 693 VAL cc_start: 0.4673 (OUTLIER) cc_final: 0.4418 (t) REVERT: C 30 GLU cc_start: 0.8222 (tt0) cc_final: 0.7689 (mt-10) REVERT: C 50 ASN cc_start: 0.8415 (m-40) cc_final: 0.8086 (m-40) REVERT: C 79 MET cc_start: 0.8551 (mmm) cc_final: 0.8205 (tpp) REVERT: C 215 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8753 (pp20) REVERT: C 313 LEU cc_start: 0.8696 (mp) cc_final: 0.8143 (tt) REVERT: C 320 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7057 (mpp80) REVERT: C 339 ARG cc_start: 0.8083 (tpt90) cc_final: 0.7849 (tpt90) REVERT: C 431 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 497 MET cc_start: 0.8009 (mmt) cc_final: 0.7636 (mmm) outliers start: 70 outliers final: 61 residues processed: 235 average time/residue: 0.1025 time to fit residues: 39.4481 Evaluate side-chains 241 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 175 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 244 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 535 ASP Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 CYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 694 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 117 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 187 optimal weight: 0.0070 chunk 167 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105311 restraints weight = 31194.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103395 restraints weight = 23646.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104312 restraints weight = 21482.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104766 restraints weight = 16490.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105532 restraints weight = 13940.419| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16626 Z= 0.191 Angle : 0.647 14.349 22566 Z= 0.321 Chirality : 0.045 0.307 2676 Planarity : 0.005 0.055 2979 Dihedral : 4.184 50.332 2351 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.28 % Rotamer: Outliers : 4.44 % Allowed : 31.03 % Favored : 64.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2184 helix: 1.11 (0.20), residues: 707 sheet: -1.35 (0.28), residues: 341 loop : -1.12 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 516 TYR 0.014 0.002 TYR A 80 PHE 0.022 0.001 PHE A 531 TRP 0.004 0.001 TRP C 173 HIS 0.004 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (16626) covalent geometry : angle 0.64748 / 0.32 (22566) hydrogen bonds : bond 0.03514 / 2.40 ( 654) hydrogen bonds : angle 4.76720 / 3.28 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2460.87 seconds wall clock time: 43 minutes 28.00 seconds (2608.00 seconds total)