Starting phenix.real_space_refine on Tue Jan 21 07:23:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wxf_37905/01_2025/8wxf_37905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wxf_37905/01_2025/8wxf_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_37905/01_2025/8wxf_37905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wxf_37905/01_2025/8wxf_37905.map" model { file = "/net/cci-nas-00/data/ceres_data/8wxf_37905/01_2025/8wxf_37905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wxf_37905/01_2025/8wxf_37905.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.46, per 1000 atoms: 0.58 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: 4.07 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.69 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: 5.30 Time building geometry restraints manager: 4.68 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: 0.06 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: 2.090 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 37.430 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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= 0.218 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), 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 TRP 0.003 0.001 TRP A 173 HIS 0.003 0.001 HIS B 409 PHE 0.014 0.001 PHE C 531 TYR 0.010 0.001 TYR B 276 ARG 0.008 0.000 ARG A 406 *********************** 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 : 1.868 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: 0.8605 (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: 0.2524 time to fit residues: 78.4084 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 : 1.856 ------------------------------------------------------------------------------- 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 184 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103776 restraints weight = 30867.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106817 restraints weight = 17837.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108858 restraints weight = 12473.562| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16626 Z= 0.202 Angle : 0.601 10.291 22566 Z= 0.310 Chirality : 0.044 0.201 2676 Planarity : 0.005 0.060 2979 Dihedral : 4.694 55.625 2357 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.13 % Favored : 94.73 % Rotamer: Outliers : 4.44 % Allowed : 28.09 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2184 helix: 0.88 (0.20), residues: 697 sheet: -1.21 (0.30), residues: 329 loop : -1.37 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 173 HIS 0.002 0.000 HIS C 694 PHE 0.018 0.001 PHE A 531 TYR 0.012 0.001 TYR B 270 ARG 0.004 0.000 ARG B 350 *********************** 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 265 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.7448 (tp30) cc_final: 0.7187 (tp30) REVERT: A 333 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8820 (tttt) REVERT: A 345 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.8519 (p90) REVERT: A 482 LEU cc_start: 0.9088 (mm) cc_final: 0.8597 (mm) REVERT: A 522 THR cc_start: 0.9318 (m) cc_final: 0.8853 (p) REVERT: B 389 MET cc_start: 0.8162 (mmm) cc_final: 0.7918 (mtt) REVERT: C 215 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8659 (pp20) REVERT: C 482 LEU cc_start: 0.8731 (mm) cc_final: 0.8302 (mm) outliers start: 77 outliers final: 36 residues processed: 244 average time/residue: 0.2440 time to fit residues: 95.0794 Evaluate side-chains 206 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 424 VAL 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 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 C residue 68 PHE 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 107 optimal weight: 0.0040 chunk 131 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 17 optimal weight: 0.0030 chunk 76 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.8008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 65 HIS B 412 ASN ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 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 = 0.3924 r_free = 0.3924 target = 0.147018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101352 restraints weight = 30721.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104280 restraints weight = 17822.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106266 restraints weight = 12498.252| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16626 Z= 0.258 Angle : 0.600 11.928 22566 Z= 0.307 Chirality : 0.044 0.190 2676 Planarity : 0.005 0.058 2979 Dihedral : 4.481 53.579 2354 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.54 % Favored : 94.32 % Rotamer: Outliers : 5.36 % Allowed : 27.57 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 2184 helix: 0.99 (0.20), residues: 703 sheet: -1.31 (0.29), residues: 330 loop : -1.31 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 173 HIS 0.002 0.001 HIS A 410 PHE 0.023 0.001 PHE B 345 TYR 0.012 0.002 TYR A 411 ARG 0.008 0.000 ARG A 516 *********************** 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 260 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 167 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8637 (m) REVERT: A 311 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8914 (mm-40) REVERT: A 522 THR cc_start: 0.9230 (m) cc_final: 0.8780 (p) REVERT: B 389 MET cc_start: 0.8322 (mmm) cc_final: 0.8110 (mtt) REVERT: B 412 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8312 (m-40) REVERT: C 30 GLU cc_start: 0.8207 (tt0) cc_final: 0.7779 (mt-10) REVERT: C 50 ASN cc_start: 0.8565 (m-40) cc_final: 0.8299 (m-40) REVERT: C 215 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8710 (pp20) REVERT: C 320 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7201 (mtm-85) outliers start: 93 outliers final: 55 residues processed: 239 average time/residue: 0.2449 time to fit residues: 93.4360 Evaluate side-chains 221 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 162 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 331 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 446 LEU 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 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 412 ASN 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 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 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 538 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 87 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 193 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 180 optimal weight: 0.0770 chunk 141 optimal weight: 0.0670 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3949 r_free = 0.3949 target = 0.148860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106846 restraints weight = 31017.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105542 restraints weight = 22194.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106194 restraints weight = 18104.413| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16626 Z= 0.192 Angle : 0.578 12.277 22566 Z= 0.292 Chirality : 0.044 0.282 2676 Planarity : 0.005 0.053 2979 Dihedral : 4.375 53.755 2354 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 4.84 % Allowed : 28.66 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 2184 helix: 1.04 (0.20), residues: 701 sheet: -1.24 (0.29), residues: 330 loop : -1.22 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 173 HIS 0.004 0.001 HIS A 344 PHE 0.023 0.001 PHE A 345 TYR 0.010 0.001 TYR B 411 ARG 0.004 0.000 ARG A 339 *********************** 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 248 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 164 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8600 (m) REVERT: A 311 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8994 (mm-40) REVERT: A 522 THR cc_start: 0.9255 (m) cc_final: 0.8762 (p) REVERT: A 643 ASP cc_start: 0.8204 (t0) cc_final: 0.7880 (t70) REVERT: B 389 MET cc_start: 0.8343 (mmm) cc_final: 0.8079 (mtt) REVERT: B 412 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8307 (m-40) REVERT: C 30 GLU cc_start: 0.8242 (tt0) cc_final: 0.7790 (mt-10) REVERT: C 204 MET cc_start: 0.8933 (tmm) cc_final: 0.8730 (tmm) REVERT: C 215 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8733 (pp20) REVERT: C 320 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6952 (mtm-85) outliers start: 84 outliers final: 57 residues processed: 232 average time/residue: 0.2371 time to fit residues: 88.7912 Evaluate side-chains 226 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 165 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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 158 SER Chi-restraints excluded: chain A residue 166 VAL 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 316 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 621 ILE 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 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 628 GLN Chi-restraints excluded: chain C residue 26 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 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 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 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 72 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 190 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.150053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108226 restraints weight = 31285.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107158 restraints weight = 22013.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108171 restraints weight = 18095.291| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16626 Z= 0.167 Angle : 0.574 14.613 22566 Z= 0.283 Chirality : 0.044 0.258 2676 Planarity : 0.004 0.053 2979 Dihedral : 4.229 52.735 2354 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 4.90 % Allowed : 28.43 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2184 helix: 1.06 (0.20), residues: 705 sheet: -1.18 (0.29), residues: 328 loop : -1.13 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 173 HIS 0.005 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.008 0.001 TYR C 80 ARG 0.003 0.000 ARG A 339 *********************** 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 264 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 179 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (m) REVERT: A 311 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8959 (mm-40) REVERT: A 522 THR cc_start: 0.9269 (m) cc_final: 0.8811 (p) REVERT: A 643 ASP cc_start: 0.8017 (t0) cc_final: 0.7803 (t70) REVERT: A 695 ILE cc_start: 0.1570 (OUTLIER) cc_final: 0.1335 (pt) REVERT: B 51 MET cc_start: 0.8341 (ttt) cc_final: 0.8094 (ttt) REVERT: C 30 GLU cc_start: 0.8187 (tt0) cc_final: 0.7813 (mt-10) REVERT: C 181 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: C 215 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8733 (pp20) REVERT: C 320 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6991 (mtm-85) outliers start: 85 outliers final: 57 residues processed: 247 average time/residue: 0.2449 time to fit residues: 95.6584 Evaluate side-chains 227 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 1.809 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 181 GLN 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 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 618 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 181 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 79 optimal weight: 0.9990 chunk 66 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 0.0170 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 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 = 0.3971 r_free = 0.3971 target = 0.150632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105869 restraints weight = 30743.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108920 restraints weight = 17476.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110989 restraints weight = 12120.413| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16626 Z= 0.158 Angle : 0.578 13.394 22566 Z= 0.281 Chirality : 0.044 0.240 2676 Planarity : 0.004 0.052 2979 Dihedral : 4.017 51.565 2353 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 3.81 % Allowed : 29.76 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 2184 helix: 1.11 (0.20), residues: 705 sheet: -1.05 (0.29), residues: 324 loop : -1.06 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 173 HIS 0.005 0.000 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.011 0.001 TYR C 276 ARG 0.003 0.000 ARG B 596 *********************** 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 244 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 178 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7692 (t0) cc_final: 0.7467 (t0) REVERT: A 303 ASP cc_start: 0.8942 (m-30) cc_final: 0.8722 (p0) REVERT: A 412 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8069 (m110) REVERT: A 643 ASP cc_start: 0.8129 (t0) cc_final: 0.7831 (t70) REVERT: A 695 ILE cc_start: 0.1528 (OUTLIER) cc_final: 0.1318 (pt) REVERT: B 208 GLU cc_start: 0.7462 (tp30) cc_final: 0.7209 (tp30) REVERT: B 590 MET cc_start: 0.5821 (tpp) cc_final: 0.5618 (tpp) REVERT: C 30 GLU cc_start: 0.8210 (tt0) cc_final: 0.7699 (mt-10) REVERT: C 181 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8347 (pm20) REVERT: C 215 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8731 (pp20) REVERT: C 320 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.6877 (mtm-85) outliers start: 66 outliers final: 51 residues processed: 231 average time/residue: 0.2403 time to fit residues: 89.6837 Evaluate side-chains 228 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 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 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 412 ASN 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 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 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 477 SER 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 181 GLN 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 50 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 206 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** B 412 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.148605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.107940 restraints weight = 31247.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.105644 restraints weight = 22977.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106760 restraints weight = 19404.232| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1814 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= 0.226 Angle : 0.593 12.776 22566 Z= 0.292 Chirality : 0.044 0.245 2676 Planarity : 0.004 0.053 2979 Dihedral : 3.888 50.268 2350 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.85 % Favored : 95.01 % Rotamer: Outliers : 4.61 % Allowed : 29.12 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 2184 helix: 1.13 (0.20), residues: 708 sheet: -1.05 (0.29), residues: 319 loop : -1.04 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 173 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.027 0.001 TYR A 411 ARG 0.003 0.000 ARG B 339 *********************** 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 252 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 172 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8032 (t0) cc_final: 0.7808 (t70) REVERT: A 643 ASP cc_start: 0.8117 (t0) cc_final: 0.7882 (t70) REVERT: A 695 ILE cc_start: 0.1576 (OUTLIER) cc_final: 0.1363 (pt) REVERT: B 47 ASP cc_start: 0.7936 (t70) cc_final: 0.7668 (t0) REVERT: B 79 MET cc_start: 0.8150 (tpp) cc_final: 0.7765 (tpp) REVERT: B 495 ILE cc_start: 0.8981 (mp) cc_final: 0.8685 (mm) REVERT: C 30 GLU cc_start: 0.8221 (tt0) cc_final: 0.7756 (mt-10) REVERT: C 50 ASN cc_start: 0.8509 (m-40) cc_final: 0.8277 (m-40) REVERT: C 181 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: C 215 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8746 (pp20) REVERT: C 320 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6921 (mtm-85) outliers start: 80 outliers final: 63 residues processed: 239 average time/residue: 0.2399 time to fit residues: 93.5422 Evaluate side-chains 237 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 2.012 ------------------------------------------------------------------------------- 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 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 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 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 311 GLN 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 519 VAL Chi-restraints excluded: chain B residue 545 VAL 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 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 68 PHE Chi-restraints excluded: chain C residue 181 GLN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 18 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 202 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 HIS ** B 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 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 = 0.3869 r_free = 0.3869 target = 0.142763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101849 restraints weight = 31582.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100008 restraints weight = 25506.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100799 restraints weight = 20821.292| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 16626 Z= 0.459 Angle : 0.741 12.481 22566 Z= 0.377 Chirality : 0.047 0.333 2676 Planarity : 0.006 0.068 2979 Dihedral : 4.502 50.664 2350 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.78 % Favored : 93.09 % Rotamer: Outliers : 5.13 % Allowed : 28.66 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 2184 helix: 0.92 (0.20), residues: 709 sheet: -1.65 (0.27), residues: 343 loop : -1.29 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 173 HIS 0.007 0.002 HIS B 409 PHE 0.023 0.002 PHE A 531 TYR 0.022 0.002 TYR A 80 ARG 0.005 0.001 ARG B 312 *********************** 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 247 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 158 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.8180 (t0) cc_final: 0.7957 (t0) REVERT: A 695 ILE cc_start: 0.1630 (OUTLIER) cc_final: 0.1401 (pt) REVERT: B 47 ASP cc_start: 0.8068 (t70) cc_final: 0.7779 (t0) REVERT: B 51 MET cc_start: 0.8292 (ttt) cc_final: 0.8029 (ttt) REVERT: B 389 MET cc_start: 0.8637 (mmm) cc_final: 0.8260 (mtt) REVERT: C 50 ASN cc_start: 0.8741 (m-40) cc_final: 0.8478 (m-40) REVERT: C 215 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8794 (pp20) REVERT: C 320 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7079 (mtm-85) REVERT: C 396 ILE cc_start: 0.8780 (pp) cc_final: 0.8563 (pt) outliers start: 89 outliers final: 71 residues processed: 227 average time/residue: 0.2323 time to fit residues: 85.8695 Evaluate side-chains 231 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 157 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 465 SER Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 535 ASP 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 141 LEU Chi-restraints excluded: chain B residue 178 THR 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 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 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 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 107 ILE 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 379 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 492 VAL Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 545 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 123 optimal weight: 0.0570 chunk 171 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** 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 = 0.3933 r_free = 0.3933 target = 0.147594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106918 restraints weight = 31115.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106074 restraints weight = 23126.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.106734 restraints weight = 19473.429| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16626 Z= 0.189 Angle : 0.625 12.775 22566 Z= 0.305 Chirality : 0.045 0.233 2676 Planarity : 0.005 0.066 2979 Dihedral : 4.159 50.899 2350 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 3.92 % Allowed : 30.28 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2184 helix: 1.07 (0.20), residues: 708 sheet: -1.35 (0.28), residues: 337 loop : -1.14 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 173 HIS 0.004 0.001 HIS A 344 PHE 0.023 0.001 PHE A 531 TYR 0.012 0.001 TYR B 276 ARG 0.004 0.000 ARG C 356 *********************** 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 245 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 177 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 318 GLU cc_start: 0.7545 (mp0) cc_final: 0.7126 (mp0) REVERT: B 208 GLU cc_start: 0.7818 (tp30) cc_final: 0.7211 (tp30) REVERT: B 389 MET cc_start: 0.8520 (mmm) cc_final: 0.7946 (mtt) REVERT: B 590 MET cc_start: 0.5642 (tpp) cc_final: 0.5349 (tpp) REVERT: C 50 ASN cc_start: 0.8476 (m-40) cc_final: 0.8196 (m-40) REVERT: C 215 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8749 (pp20) REVERT: C 320 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6837 (mtm180) REVERT: C 396 ILE cc_start: 0.8707 (pp) cc_final: 0.8502 (pt) REVERT: C 431 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7548 (tm-30) outliers start: 68 outliers final: 60 residues processed: 231 average time/residue: 0.2879 time to fit residues: 108.9400 Evaluate side-chains 229 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 331 LEU Chi-restraints excluded: chain A residue 345 PHE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 43 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 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 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 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 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 373 LEU Chi-restraints excluded: chain C residue 465 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 72 optimal weight: 0.9980 chunk 217 optimal weight: 0.0570 chunk 202 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 ASN ** 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 = 0.3938 r_free = 0.3938 target = 0.147892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.102665 restraints weight = 30701.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105679 restraints weight = 17651.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107667 restraints weight = 12299.058| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2208 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= 0.181 Angle : 0.621 12.337 22566 Z= 0.303 Chirality : 0.044 0.278 2676 Planarity : 0.005 0.064 2979 Dihedral : 4.035 49.898 2350 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.81 % Favored : 95.05 % Rotamer: Outliers : 3.86 % Allowed : 30.22 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2184 helix: 1.11 (0.20), residues: 707 sheet: -1.30 (0.28), residues: 337 loop : -1.05 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 173 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.008 0.001 TYR B 80 ARG 0.003 0.000 ARG A 301 ********************** 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 241 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7474 (mp0) cc_final: 0.7060 (mp0) REVERT: B 208 GLU cc_start: 0.7666 (tp30) cc_final: 0.7159 (tp30) REVERT: B 590 MET cc_start: 0.5712 (tpp) cc_final: 0.5366 (tpp) REVERT: C 30 GLU cc_start: 0.8240 (tt0) cc_final: 0.7697 (mt-10) REVERT: C 50 ASN cc_start: 0.8543 (m-40) cc_final: 0.8272 (m-40) REVERT: C 215 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8775 (pp20) REVERT: C 313 LEU cc_start: 0.8686 (mp) cc_final: 0.8117 (tt) REVERT: C 320 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7055 (mpp80) outliers start: 67 outliers final: 61 residues processed: 229 average time/residue: 0.2386 time to fit residues: 87.9011 Evaluate side-chains 233 residues out of total 1734 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 2.013 ------------------------------------------------------------------------------- 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 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 538 VAL Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain B residue 43 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 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 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 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 492 VAL Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 140 optimal weight: 0.0170 chunk 4 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 chunk 116 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 83 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** 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 = 0.4215 r_free = 0.4215 target = 0.164230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115094 restraints weight = 31903.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.118787 restraints weight = 17723.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121099 restraints weight = 12168.990| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2342 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= 0.162 Angle : 0.615 11.826 22566 Z= 0.298 Chirality : 0.044 0.207 2676 Planarity : 0.004 0.058 2979 Dihedral : 3.966 48.824 2350 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.21 % Favored : 95.65 % Rotamer: Outliers : 3.29 % Allowed : 30.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2184 helix: 1.09 (0.20), residues: 707 sheet: -1.19 (0.28), residues: 340 loop : -0.98 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 173 HIS 0.004 0.001 HIS A 344 PHE 0.022 0.001 PHE A 531 TYR 0.011 0.001 TYR C 138 ARG 0.003 0.000 ARG C 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4666.96 seconds wall clock time: 84 minutes 49.57 seconds (5089.57 seconds total)