Starting phenix.real_space_refine on Thu Aug 6 06:04:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhl_61486/08_2026/9jhl_61486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhl_61486/08_2026/9jhl_61486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhl_61486/08_2026/9jhl_61486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhl_61486/08_2026/9jhl_61486.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhl_61486/08_2026/9jhl_61486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhl_61486/08_2026/9jhl_61486.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 70 5.49 5 S 40 5.16 5 C 8488 2.51 5 N 2230 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13512 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, D, F Time building chain proxies: 5.47, per 1000 atoms: 0.40 Number of scatterers: 13512 At special positions: 0 Unit cell: (120.54, 94.3, 101.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 40 16.00 P 70 15.00 O 2680 8.00 N 2230 7.00 C 8488 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: 0.84 Conformation dependent library (CDL) restraints added in 478.2 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 24 sheets defined 31.4% alpha, 22.1% beta 28 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 97 through 115 removed outlier: 4.075A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 507 through 523 removed outlier: 4.026A pdb=" N TYR A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 603 Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.660A pdb=" N LYS A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'B' and resid 43 through 54 Processing helix chain 'B' and resid 97 through 115 removed outlier: 4.076A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 388 through 404 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 493 through 503 Processing helix chain 'B' and resid 507 through 523 removed outlier: 4.026A pdb=" N TYR B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 603 Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.660A pdb=" N LYS B 631 " --> pdb=" O TYR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 711 Processing helix chain 'B' and resid 723 through 735 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 125 through 127 removed outlier: 3.583A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS A 148 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.583A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 328 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.550A pdb=" N PHE A 26 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER A 89 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.604A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 removed outlier: 6.610A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP A 562 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU A 567 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.640A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.300A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N GLU A 433 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 removed outlier: 6.300A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.583A pdb=" N LEU B 134 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 148 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.583A pdb=" N LEU B 134 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL B 172 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 328 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.549A pdb=" N PHE B 26 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER B 89 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AB9, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AC1, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.605A pdb=" N TYR B 271 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.609A pdb=" N ILE B 637 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS B 539 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS B 612 " --> pdb=" O CYS B 539 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL B 541 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA B 614 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 543 " --> pdb=" O ALA B 614 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 562 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU B 567 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 358 through 359 removed outlier: 4.641A pdb=" N LEU B 352 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 423 through 424 removed outlier: 6.299A pdb=" N VAL B 378 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLU B 433 " --> pdb=" O PHE B 380 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 382 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR B 435 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR B 384 " --> pdb=" O TYR B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 423 through 424 removed outlier: 6.299A pdb=" N VAL B 378 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 407 through 408 496 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3230 1.33 - 1.45: 2983 1.45 - 1.57: 7507 1.57 - 1.69: 136 1.69 - 1.81: 70 Bond restraints: 13926 Sorted by residual: bond pdb=" C3' DG D 15 " pdb=" O3' DG D 15 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.83e+01 bond pdb=" C3' DG C 15 " pdb=" O3' DG C 15 " ideal model delta sigma weight residual 1.435 1.490 -0.055 1.30e-02 5.92e+03 1.80e+01 bond pdb=" C3' DC E 8 " pdb=" O3' DC E 8 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.55e+01 bond pdb=" C3' DC F 8 " pdb=" O3' DC F 8 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 1.529 1.493 0.036 1.00e-02 1.00e+04 1.33e+01 ... (remaining 13921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18325 2.18 - 4.37: 662 4.37 - 6.55: 65 6.55 - 8.74: 16 8.74 - 10.92: 4 Bond angle restraints: 19072 Sorted by residual: angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 102.60 3.40 6.00e-01 2.78e+00 3.20e+01 angle pdb=" O4' DG D 4 " pdb=" C4' DG D 4 " pdb=" C3' DG D 4 " ideal model delta sigma weight residual 106.00 102.65 3.35 6.00e-01 2.78e+00 3.12e+01 angle pdb=" O4' DA F 5 " pdb=" C4' DA F 5 " pdb=" C3' DA F 5 " ideal model delta sigma weight residual 106.00 102.76 3.24 6.00e-01 2.78e+00 2.92e+01 angle pdb=" O4' DT D 9 " pdb=" C4' DT D 9 " pdb=" C3' DT D 9 " ideal model delta sigma weight residual 106.00 102.76 3.24 6.00e-01 2.78e+00 2.92e+01 angle pdb=" O4' DT C 9 " pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 106.00 102.76 3.24 6.00e-01 2.78e+00 2.91e+01 ... (remaining 19067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.88: 7928 31.88 - 63.76: 326 63.76 - 95.64: 8 95.64 - 127.52: 0 127.52 - 159.40: 2 Dihedral angle restraints: 8264 sinusoidal: 3890 harmonic: 4374 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual 180.00 -143.31 -36.69 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA GLU B 470 " pdb=" C GLU B 470 " pdb=" N ILE B 471 " pdb=" CA ILE B 471 " ideal model delta harmonic sigma weight residual -180.00 -143.32 -36.68 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CA ILE A 471 " pdb=" C ILE A 471 " pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 8261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1489 0.056 - 0.111: 463 0.111 - 0.167: 108 0.167 - 0.223: 21 0.223 - 0.278: 7 Chirality restraints: 2088 Sorted by residual: chirality pdb=" CB ILE B 44 " pdb=" CA ILE B 44 " pdb=" CG1 ILE B 44 " pdb=" CG2 ILE B 44 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE A 44 " pdb=" CA ILE A 44 " pdb=" CG1 ILE A 44 " pdb=" CG2 ILE A 44 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE B 651 " pdb=" CA ILE B 651 " pdb=" CG1 ILE B 651 " pdb=" CG2 ILE B 651 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2085 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " -0.024 2.00e-02 2.50e+03 1.52e-02 5.78e+00 pdb=" CG TRP B 623 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " 0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " 0.024 2.00e-02 2.50e+03 1.52e-02 5.78e+00 pdb=" CG TRP A 623 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 513 " -0.016 2.00e-02 2.50e+03 1.94e-02 5.67e+00 pdb=" CG HIS B 513 " 0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS B 513 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 513 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS B 513 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 513 " -0.002 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 65 2.49 - 3.09: 8594 3.09 - 3.69: 21370 3.69 - 4.30: 33453 4.30 - 4.90: 53433 Nonbonded interactions: 116915 Sorted by model distance: nonbonded pdb=" OD2 ASP B 544 " pdb="MN MN B 801 " model vdw 1.885 2.320 nonbonded pdb=" OD2 ASP A 544 " pdb="MN MN A 801 " model vdw 1.912 2.320 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.924 2.320 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.939 2.320 nonbonded pdb=" OP1 DA D 3 " pdb="MN MN D 801 " model vdw 1.940 2.320 ... (remaining 116910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 16.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.008 0.097 13926 Z= 0.444 Angle : 0.922 10.920 19072 Z= 0.596 Chirality : 0.059 0.278 2088 Planarity : 0.006 0.047 2180 Dihedral : 14.628 159.401 5476 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.18), residues: 1486 helix: -2.18 (0.19), residues: 430 sheet: -1.95 (0.25), residues: 348 loop : -1.23 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 618 TYR 0.030 0.003 TYR A 624 PHE 0.037 0.004 PHE B 432 TRP 0.035 0.006 TRP A 623 HIS 0.024 0.005 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.44 (13926) covalent geometry : angle 0.92188 / 0.60 (19072) hydrogen bonds : bond 0.19805 / 12.62 ( 554) hydrogen bonds : angle 8.73998 / 5.93 ( 1540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 254 average time/residue: 0.6367 time to fit residues: 175.0216 Evaluate side-chains 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 96 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 265 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 612 HIS ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 ASN B 136 ASN B 265 ASN ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 612 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.064962 restraints weight = 29283.724| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.21 r_work: 0.2869 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13926 Z= 0.185 Angle : 0.695 6.495 19072 Z= 0.391 Chirality : 0.048 0.249 2088 Planarity : 0.004 0.054 2180 Dihedral : 17.874 163.349 2402 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.80 % Allowed : 10.93 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.20), residues: 1486 helix: -0.59 (0.22), residues: 438 sheet: -1.60 (0.26), residues: 332 loop : -0.71 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 743 TYR 0.019 0.002 TYR B 511 PHE 0.017 0.002 PHE A 388 TRP 0.022 0.003 TRP A 623 HIS 0.009 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (13926) covalent geometry : angle 0.69550 / 0.39 (19072) hydrogen bonds : bond 0.05307 / 3.41 ( 554) hydrogen bonds : angle 6.14538 / 4.09 ( 1540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.338 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 78 ASP cc_start: 0.9137 (t0) cc_final: 0.8880 (t0) REVERT: A 98 MET cc_start: 0.8559 (mmt) cc_final: 0.8170 (mmm) REVERT: A 193 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8971 (mmtm) REVERT: A 271 TYR cc_start: 0.5920 (m-10) cc_final: 0.5696 (m-10) REVERT: A 418 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9133 (mp0) REVERT: A 552 ILE cc_start: 0.8809 (mt) cc_final: 0.8558 (mp) REVERT: A 585 GLU cc_start: 0.8300 (mp0) cc_final: 0.8052 (mp0) REVERT: B 78 ASP cc_start: 0.9140 (t0) cc_final: 0.8885 (t0) REVERT: B 98 MET cc_start: 0.8537 (mmt) cc_final: 0.8148 (mmm) REVERT: B 552 ILE cc_start: 0.8814 (mt) cc_final: 0.8517 (mp) REVERT: B 585 GLU cc_start: 0.8300 (mp0) cc_final: 0.8038 (mp0) outliers start: 24 outliers final: 9 residues processed: 159 average time/residue: 0.5054 time to fit residues: 88.2670 Evaluate side-chains 110 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 539 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 0.0370 chunk 116 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN A 409 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 409 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.087455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063695 restraints weight = 29756.124| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.21 r_work: 0.2847 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13926 Z= 0.203 Angle : 0.646 6.580 19072 Z= 0.364 Chirality : 0.047 0.270 2088 Planarity : 0.003 0.030 2180 Dihedral : 17.598 161.964 2398 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.77 % Allowed : 11.68 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1486 helix: 0.19 (0.23), residues: 444 sheet: -1.16 (0.29), residues: 276 loop : -0.45 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 504 TYR 0.023 0.002 TYR B 237 PHE 0.013 0.002 PHE A 591 TRP 0.012 0.002 TRP A 623 HIS 0.011 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (13926) covalent geometry : angle 0.64618 / 0.36 (19072) hydrogen bonds : bond 0.04586 / 2.92 ( 554) hydrogen bonds : angle 5.67008 / 3.77 ( 1540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.466 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 78 ASP cc_start: 0.9169 (t0) cc_final: 0.8888 (t0) REVERT: A 98 MET cc_start: 0.8618 (mmt) cc_final: 0.8237 (mmm) REVERT: A 151 ASN cc_start: 0.9292 (m-40) cc_final: 0.8707 (p0) REVERT: A 193 LYS cc_start: 0.9340 (ttmm) cc_final: 0.8991 (mmmm) REVERT: A 356 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8731 (mtmm) REVERT: A 552 ILE cc_start: 0.8752 (mt) cc_final: 0.8502 (mp) REVERT: A 585 GLU cc_start: 0.8446 (mp0) cc_final: 0.8123 (mp0) REVERT: A 630 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9125 (mtmm) REVERT: B 78 ASP cc_start: 0.9190 (t0) cc_final: 0.8911 (t0) REVERT: B 98 MET cc_start: 0.8606 (mmt) cc_final: 0.8208 (mmm) REVERT: B 356 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8729 (mtmm) REVERT: B 552 ILE cc_start: 0.8762 (mt) cc_final: 0.8510 (mp) REVERT: B 585 GLU cc_start: 0.8388 (mp0) cc_final: 0.8055 (mp0) outliers start: 37 outliers final: 14 residues processed: 148 average time/residue: 0.4641 time to fit residues: 76.1809 Evaluate side-chains 123 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS A 364 GLN ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 274 HIS B 364 GLN ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064522 restraints weight = 29549.700| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.28 r_work: 0.2806 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13926 Z= 0.195 Angle : 0.625 7.062 19072 Z= 0.350 Chirality : 0.046 0.265 2088 Planarity : 0.003 0.029 2180 Dihedral : 17.504 161.983 2398 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 13.10 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1486 helix: 0.71 (0.24), residues: 444 sheet: -1.39 (0.30), residues: 246 loop : -0.28 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 393 TYR 0.030 0.002 TYR B 237 PHE 0.014 0.002 PHE B 81 TRP 0.012 0.002 TRP B 482 HIS 0.006 0.002 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (13926) covalent geometry : angle 0.62487 / 0.35 (19072) hydrogen bonds : bond 0.04144 / 2.64 ( 554) hydrogen bonds : angle 5.39363 / 3.59 ( 1540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9256 (t0) cc_final: 0.9040 (t0) REVERT: A 98 MET cc_start: 0.8621 (mmt) cc_final: 0.8376 (mmt) REVERT: A 151 ASN cc_start: 0.9362 (m-40) cc_final: 0.8734 (p0) REVERT: A 552 ILE cc_start: 0.8661 (mt) cc_final: 0.8383 (mp) REVERT: A 630 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9152 (mtpm) REVERT: B 78 ASP cc_start: 0.9254 (t0) cc_final: 0.9041 (t0) REVERT: B 98 MET cc_start: 0.8620 (mmt) cc_final: 0.8402 (mmt) REVERT: B 151 ASN cc_start: 0.9358 (m-40) cc_final: 0.8700 (p0) REVERT: B 552 ILE cc_start: 0.8657 (mt) cc_final: 0.8374 (mp) outliers start: 28 outliers final: 18 residues processed: 136 average time/residue: 0.4238 time to fit residues: 64.2702 Evaluate side-chains 110 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 451 ASN ** 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 = 0.3477 r_free = 0.3477 target = 0.089427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.065941 restraints weight = 29681.820| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.30 r_work: 0.2839 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13926 Z= 0.149 Angle : 0.609 9.410 19072 Z= 0.343 Chirality : 0.046 0.259 2088 Planarity : 0.003 0.030 2180 Dihedral : 17.438 161.592 2398 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.62 % Allowed : 12.95 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1486 helix: 0.98 (0.24), residues: 442 sheet: -1.26 (0.30), residues: 250 loop : -0.23 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 56 TYR 0.029 0.001 TYR B 237 PHE 0.013 0.001 PHE A 61 TRP 0.021 0.002 TRP B 482 HIS 0.008 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (13926) covalent geometry : angle 0.60894 / 0.34 (19072) hydrogen bonds : bond 0.03859 / 2.43 ( 554) hydrogen bonds : angle 5.20682 / 3.45 ( 1540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8603 (mmt) cc_final: 0.8196 (mmt) REVERT: A 151 ASN cc_start: 0.9314 (m-40) cc_final: 0.8693 (p0) REVERT: A 179 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8573 (p) REVERT: A 365 ILE cc_start: 0.9445 (tp) cc_final: 0.9230 (tp) REVERT: A 430 CYS cc_start: 0.7136 (m) cc_final: 0.6318 (m) REVERT: A 552 ILE cc_start: 0.8645 (mt) cc_final: 0.8363 (mp) REVERT: A 630 LYS cc_start: 0.9318 (mmmm) cc_final: 0.9117 (mtpm) REVERT: B 98 MET cc_start: 0.8624 (mmt) cc_final: 0.8293 (mmt) REVERT: B 151 ASN cc_start: 0.9370 (m-40) cc_final: 0.8688 (p0) REVERT: B 179 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8562 (p) REVERT: B 365 ILE cc_start: 0.9446 (tp) cc_final: 0.9231 (tp) REVERT: B 430 CYS cc_start: 0.7115 (m) cc_final: 0.6310 (m) REVERT: B 552 ILE cc_start: 0.8659 (mt) cc_final: 0.8381 (mp) outliers start: 35 outliers final: 17 residues processed: 134 average time/residue: 0.4526 time to fit residues: 67.2480 Evaluate side-chains 123 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 HIS ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.082863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059406 restraints weight = 30082.752| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.24 r_work: 0.2735 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 13926 Z= 0.406 Angle : 0.722 9.627 19072 Z= 0.393 Chirality : 0.050 0.271 2088 Planarity : 0.004 0.052 2180 Dihedral : 17.494 161.288 2398 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.62 % Allowed : 13.92 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.22), residues: 1486 helix: 1.08 (0.24), residues: 442 sheet: -1.12 (0.32), residues: 226 loop : -0.06 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 56 TYR 0.015 0.002 TYR B 237 PHE 0.020 0.002 PHE B 591 TRP 0.007 0.002 TRP A 623 HIS 0.008 0.003 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.41 (13926) covalent geometry : angle 0.72244 / 0.39 (19072) hydrogen bonds : bond 0.04230 / 2.72 ( 554) hydrogen bonds : angle 5.30933 / 3.54 ( 1540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8690 (mmt) cc_final: 0.8338 (mmt) REVERT: A 151 ASN cc_start: 0.9350 (m-40) cc_final: 0.8762 (p0) REVERT: A 234 LEU cc_start: 0.9439 (mt) cc_final: 0.8948 (pp) REVERT: A 418 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9141 (mp0) REVERT: A 552 ILE cc_start: 0.8610 (mt) cc_final: 0.8236 (mp) REVERT: A 601 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: A 630 LYS cc_start: 0.9407 (mmmm) cc_final: 0.9205 (mtpm) REVERT: B 98 MET cc_start: 0.8698 (mmt) cc_final: 0.8299 (mmt) REVERT: B 151 ASN cc_start: 0.9362 (m-40) cc_final: 0.8722 (p0) REVERT: B 234 LEU cc_start: 0.9482 (mt) cc_final: 0.8992 (pp) REVERT: B 418 GLU cc_start: 0.9483 (mt-10) cc_final: 0.9163 (mp0) REVERT: B 552 ILE cc_start: 0.8621 (mt) cc_final: 0.8261 (mp) outliers start: 35 outliers final: 18 residues processed: 114 average time/residue: 0.3947 time to fit residues: 50.4979 Evaluate side-chains 99 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 539 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN B 577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.064323 restraints weight = 29491.770| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.24 r_work: 0.2798 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13926 Z= 0.158 Angle : 0.625 9.571 19072 Z= 0.348 Chirality : 0.046 0.260 2088 Planarity : 0.003 0.029 2180 Dihedral : 17.435 162.550 2398 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 14.37 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.22), residues: 1486 helix: 1.33 (0.25), residues: 442 sheet: -1.04 (0.32), residues: 226 loop : -0.03 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.019 0.001 TYR A 554 PHE 0.013 0.001 PHE A 314 TRP 0.009 0.001 TRP B 482 HIS 0.009 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (13926) covalent geometry : angle 0.62503 / 0.35 (19072) hydrogen bonds : bond 0.03794 / 2.40 ( 554) hydrogen bonds : angle 5.06185 / 3.36 ( 1540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8668 (mmt) cc_final: 0.8410 (mmt) REVERT: A 234 LEU cc_start: 0.9428 (mt) cc_final: 0.8913 (pp) REVERT: A 552 ILE cc_start: 0.8619 (mt) cc_final: 0.8117 (mm) REVERT: A 601 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: A 630 LYS cc_start: 0.9348 (mmmm) cc_final: 0.9129 (mtpm) REVERT: A 697 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8125 (pp) REVERT: B 98 MET cc_start: 0.8673 (mmt) cc_final: 0.8445 (mmt) REVERT: B 151 ASN cc_start: 0.9365 (m-40) cc_final: 0.8686 (p0) REVERT: B 234 LEU cc_start: 0.9478 (mt) cc_final: 0.8981 (pp) REVERT: B 266 LYS cc_start: 0.9437 (mppt) cc_final: 0.9055 (pttt) REVERT: B 552 ILE cc_start: 0.8616 (mt) cc_final: 0.8118 (mm) REVERT: B 697 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8128 (pp) outliers start: 32 outliers final: 17 residues processed: 119 average time/residue: 0.4001 time to fit residues: 53.4144 Evaluate side-chains 117 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3431 r_free = 0.3431 target = 0.086497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.063156 restraints weight = 29296.417| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.23 r_work: 0.2791 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 13926 Z= 0.203 Angle : 0.638 11.593 19072 Z= 0.351 Chirality : 0.046 0.256 2088 Planarity : 0.003 0.066 2180 Dihedral : 17.363 161.229 2398 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.54 % Allowed : 14.97 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1486 helix: 1.48 (0.25), residues: 442 sheet: -0.98 (0.33), residues: 226 loop : 0.02 (0.23), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 56 TYR 0.015 0.001 TYR A 554 PHE 0.017 0.001 PHE B 591 TRP 0.009 0.001 TRP B 528 HIS 0.007 0.002 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (13926) covalent geometry : angle 0.63848 / 0.35 (19072) hydrogen bonds : bond 0.03794 / 2.40 ( 554) hydrogen bonds : angle 4.98500 / 3.31 ( 1540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8667 (mmt) cc_final: 0.8226 (mmt) REVERT: A 234 LEU cc_start: 0.9428 (mt) cc_final: 0.8897 (pp) REVERT: A 418 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9127 (mp0) REVERT: A 552 ILE cc_start: 0.8615 (mt) cc_final: 0.8120 (mm) REVERT: A 601 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: A 697 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8153 (pp) REVERT: B 98 MET cc_start: 0.8696 (mmt) cc_final: 0.8461 (mmt) REVERT: B 151 ASN cc_start: 0.9357 (m-40) cc_final: 0.8683 (p0) REVERT: B 234 LEU cc_start: 0.9475 (mt) cc_final: 0.8955 (pp) REVERT: B 266 LYS cc_start: 0.9443 (mppt) cc_final: 0.9241 (pmtt) REVERT: B 418 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9129 (mp0) REVERT: B 552 ILE cc_start: 0.8620 (mt) cc_final: 0.8122 (mm) REVERT: B 601 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: B 697 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8147 (pp) outliers start: 34 outliers final: 17 residues processed: 126 average time/residue: 0.5168 time to fit residues: 72.1764 Evaluate side-chains 116 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 237 TYR Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3448 r_free = 0.3448 target = 0.087517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064219 restraints weight = 29535.813| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.26 r_work: 0.2805 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13926 Z= 0.162 Angle : 0.648 13.515 19072 Z= 0.355 Chirality : 0.046 0.251 2088 Planarity : 0.004 0.112 2180 Dihedral : 17.210 161.243 2398 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.87 % Allowed : 16.09 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.22), residues: 1486 helix: 1.48 (0.25), residues: 444 sheet: -0.89 (0.33), residues: 230 loop : 0.04 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 56 TYR 0.036 0.001 TYR B 108 PHE 0.017 0.001 PHE B 61 TRP 0.007 0.001 TRP B 482 HIS 0.008 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (13926) covalent geometry : angle 0.64813 / 0.35 (19072) hydrogen bonds : bond 0.03715 / 2.33 ( 554) hydrogen bonds : angle 4.91318 / 3.26 ( 1540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8658 (mmt) cc_final: 0.8233 (mmt) REVERT: A 418 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9115 (mp0) REVERT: A 533 MET cc_start: 0.9236 (tpp) cc_final: 0.8769 (tpt) REVERT: A 552 ILE cc_start: 0.8557 (mt) cc_final: 0.8075 (mm) REVERT: A 601 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: A 697 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8128 (pp) REVERT: B 98 MET cc_start: 0.8667 (mmt) cc_final: 0.8426 (mmt) REVERT: B 151 ASN cc_start: 0.9365 (m-40) cc_final: 0.8680 (p0) REVERT: B 234 LEU cc_start: 0.9459 (mt) cc_final: 0.8920 (pp) REVERT: B 418 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9115 (mp0) REVERT: B 533 MET cc_start: 0.9239 (tpp) cc_final: 0.8770 (tpt) REVERT: B 552 ILE cc_start: 0.8539 (mt) cc_final: 0.8059 (mm) REVERT: B 601 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: B 697 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8139 (pp) outliers start: 25 outliers final: 17 residues processed: 119 average time/residue: 0.4587 time to fit residues: 60.7856 Evaluate side-chains 117 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 380 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** 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 = 0.3442 r_free = 0.3442 target = 0.087146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.063784 restraints weight = 29430.601| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.24 r_work: 0.2800 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13926 Z= 0.190 Angle : 0.669 13.969 19072 Z= 0.359 Chirality : 0.046 0.258 2088 Planarity : 0.003 0.026 2180 Dihedral : 17.159 160.650 2398 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 16.09 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.22), residues: 1486 helix: 1.50 (0.25), residues: 444 sheet: -1.01 (0.33), residues: 230 loop : 0.16 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 56 TYR 0.036 0.001 TYR A 108 PHE 0.016 0.001 PHE A 591 TRP 0.006 0.001 TRP B 623 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (13926) covalent geometry : angle 0.66933 / 0.36 (19072) hydrogen bonds : bond 0.03710 / 2.32 ( 554) hydrogen bonds : angle 4.87180 / 3.24 ( 1540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8666 (mmt) cc_final: 0.8310 (mmt) REVERT: A 418 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9121 (mp0) REVERT: A 505 ASP cc_start: 0.8995 (p0) cc_final: 0.8780 (p0) REVERT: A 533 MET cc_start: 0.9239 (tpp) cc_final: 0.8781 (tpt) REVERT: A 552 ILE cc_start: 0.8556 (mt) cc_final: 0.8178 (mp) REVERT: A 601 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: A 697 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8134 (pp) REVERT: B 98 MET cc_start: 0.8677 (mmt) cc_final: 0.8434 (mmt) REVERT: B 151 ASN cc_start: 0.9361 (m-40) cc_final: 0.8676 (p0) REVERT: B 234 LEU cc_start: 0.9467 (mt) cc_final: 0.8965 (pp) REVERT: B 266 LYS cc_start: 0.6977 (pmtt) cc_final: 0.6714 (pmtt) REVERT: B 418 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9127 (mp0) REVERT: B 533 MET cc_start: 0.9243 (tpp) cc_final: 0.8783 (tpt) REVERT: B 552 ILE cc_start: 0.8548 (mt) cc_final: 0.8198 (mp) REVERT: B 601 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 697 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8135 (pp) outliers start: 28 outliers final: 20 residues processed: 123 average time/residue: 0.4656 time to fit residues: 63.4265 Evaluate side-chains 119 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 451 ASN ** 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 = 0.3492 r_free = 0.3492 target = 0.088513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065159 restraints weight = 29564.539| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.19 r_work: 0.2856 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13926 Z= 0.158 Angle : 0.675 13.643 19072 Z= 0.362 Chirality : 0.046 0.262 2088 Planarity : 0.003 0.028 2180 Dihedral : 17.098 160.336 2398 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.95 % Allowed : 16.54 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1486 helix: 1.52 (0.25), residues: 444 sheet: -0.91 (0.33), residues: 234 loop : 0.14 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 56 TYR 0.033 0.001 TYR A 108 PHE 0.014 0.001 PHE A 591 TRP 0.007 0.001 TRP B 482 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (13926) covalent geometry : angle 0.67481 / 0.36 (19072) hydrogen bonds : bond 0.03603 / 2.25 ( 554) hydrogen bonds : angle 4.80391 / 3.19 ( 1540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.62 seconds wall clock time: 51 minutes 30.44 seconds (3090.44 seconds total)