Starting phenix.real_space_refine on Fri Jul 3 11:20:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhl_61486/07_2026/9jhl_61486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhl_61486/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jhl_61486/07_2026/9jhl_61486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhl_61486/07_2026/9jhl_61486.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhl_61486/07_2026/9jhl_61486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhl_61486/07_2026/9jhl_61486.map" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Restraints were copied for chains: B, D, F Time building chain proxies: 5.23, per 1000 atoms: 0.39 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: 1.02 Conformation dependent library (CDL) restraints added in 514.9 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: 1.73 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: 3.21 Time building geometry restraints manager: 1.41 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 3.060 nonbonded pdb=" OD2 ASP A 544 " pdb="MN MN A 801 " model vdw 1.912 3.060 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.924 3.060 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.939 3.060 nonbonded pdb=" OP1 DA D 3 " pdb="MN MN D 801 " model vdw 1.940 3.060 ... (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: 0.01 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.100 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.150 ------------------------------------------------------------------------------- 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= 0.443 Angle : 0.922 10.920 19072 Z= 0.595 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 0.92150 / 0.59 (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 : 0.299 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: 0.5832 time to fit residues: 160.4845 Evaluate side-chains 136 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.090570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.066231 restraints weight = 29018.200| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.27 r_work: 0.2871 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13926 Z= 0.190 Angle : 0.693 6.810 19072 Z= 0.392 Chirality : 0.048 0.238 2088 Planarity : 0.005 0.054 2180 Dihedral : 17.901 163.838 2402 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.72 % Allowed : 10.78 % Favored : 87.50 % 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: -1.35 (0.20), residues: 1486 helix: -0.59 (0.22), residues: 438 sheet: -1.49 (0.28), residues: 302 loop : -0.67 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 743 TYR 0.020 0.002 TYR B 511 PHE 0.017 0.002 PHE A 388 TRP 0.022 0.002 TRP A 623 HIS 0.009 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (13926) covalent geometry : angle 0.69251 / 0.39 (19072) hydrogen bonds : bond 0.05313 / 3.40 ( 554) hydrogen bonds : angle 6.15948 / 4.10 ( 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 162 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.489 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: 0.9165 (t0) cc_final: 0.8903 (t0) REVERT: A 98 MET cc_start: 0.8536 (mmt) cc_final: 0.8181 (mmt) REVERT: A 193 LYS cc_start: 0.9326 (ttmm) cc_final: 0.8962 (mmtm) REVERT: A 271 TYR cc_start: 0.5937 (m-10) cc_final: 0.5725 (m-10) REVERT: A 353 MET cc_start: 0.8875 (mmm) cc_final: 0.8665 (mmm) REVERT: A 418 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9131 (mp0) REVERT: A 552 ILE cc_start: 0.8785 (mt) cc_final: 0.8543 (mp) REVERT: A 585 GLU cc_start: 0.8303 (mp0) cc_final: 0.8055 (mp0) REVERT: B 78 ASP cc_start: 0.9174 (t0) cc_final: 0.8914 (t0) REVERT: B 98 MET cc_start: 0.8517 (mmt) cc_final: 0.8159 (mmm) REVERT: B 193 LYS cc_start: 0.9322 (ttmm) cc_final: 0.8949 (mmtm) REVERT: B 271 TYR cc_start: 0.5838 (m-10) cc_final: 0.5637 (m-10) REVERT: B 353 MET cc_start: 0.8881 (mmm) cc_final: 0.8672 (mmm) REVERT: B 552 ILE cc_start: 0.8800 (mt) cc_final: 0.8557 (mp) REVERT: B 585 GLU cc_start: 0.8299 (mp0) cc_final: 0.8038 (mp0) outliers start: 23 outliers final: 9 residues processed: 157 average time/residue: 0.5296 time to fit residues: 91.3775 Evaluate side-chains 111 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 3.9990 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.0670 chunk 116 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.086983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063005 restraints weight = 29834.407| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.27 r_work: 0.2773 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13926 Z= 0.281 Angle : 0.685 6.492 19072 Z= 0.382 Chirality : 0.048 0.256 2088 Planarity : 0.004 0.030 2180 Dihedral : 17.650 162.521 2398 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.77 % Allowed : 11.38 % Favored : 85.85 % 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: -0.67 (0.21), residues: 1486 helix: 0.27 (0.24), residues: 444 sheet: -1.31 (0.29), residues: 288 loop : -0.40 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 504 TYR 0.024 0.002 TYR B 237 PHE 0.017 0.002 PHE A 388 TRP 0.013 0.002 TRP A 623 HIS 0.013 0.003 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.28 (13926) covalent geometry : angle 0.68484 / 0.38 (19072) hydrogen bonds : bond 0.04659 / 2.98 ( 554) hydrogen bonds : angle 5.65620 / 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 150 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.364 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 98 MET cc_start: 0.8605 (mmt) cc_final: 0.8403 (mmt) REVERT: A 151 ASN cc_start: 0.9384 (m-40) cc_final: 0.8775 (p0) REVERT: A 193 LYS cc_start: 0.9339 (ttmm) cc_final: 0.8985 (mmmm) REVERT: A 356 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8751 (mtmm) REVERT: A 552 ILE cc_start: 0.8693 (mt) cc_final: 0.8421 (mp) REVERT: A 585 GLU cc_start: 0.8496 (mp0) cc_final: 0.8132 (mp0) REVERT: A 630 LYS cc_start: 0.9393 (mmmm) cc_final: 0.9189 (mtpm) REVERT: A 660 GLU cc_start: 0.8455 (mp0) cc_final: 0.8225 (mp0) REVERT: B 56 ARG cc_start: 0.8595 (ptm-80) cc_final: 0.8394 (tmm160) REVERT: B 98 MET cc_start: 0.8613 (mmt) cc_final: 0.8252 (mmt) REVERT: B 193 LYS cc_start: 0.9340 (ttmm) cc_final: 0.8976 (mmmm) REVERT: B 356 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8758 (mtmm) REVERT: B 552 ILE cc_start: 0.8719 (mt) cc_final: 0.8432 (mp) REVERT: B 585 GLU cc_start: 0.8442 (mp0) cc_final: 0.8085 (mp0) REVERT: B 630 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9140 (mtmm) outliers start: 37 outliers final: 14 residues processed: 144 average time/residue: 0.4988 time to fit residues: 79.1160 Evaluate side-chains 117 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 0.8980 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 145 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3452 r_free = 0.3452 target = 0.088138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.064199 restraints weight = 29583.546| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.29 r_work: 0.2800 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13926 Z= 0.188 Angle : 0.623 8.089 19072 Z= 0.350 Chirality : 0.046 0.245 2088 Planarity : 0.003 0.029 2180 Dihedral : 17.574 163.108 2398 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.17 % Allowed : 12.65 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.21), residues: 1486 helix: 0.72 (0.24), residues: 444 sheet: -1.40 (0.30), residues: 246 loop : -0.21 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 56 TYR 0.027 0.001 TYR B 237 PHE 0.014 0.002 PHE A 57 TRP 0.012 0.001 TRP B 482 HIS 0.005 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (13926) covalent geometry : angle 0.62325 / 0.35 (19072) hydrogen bonds : bond 0.04110 / 2.61 ( 554) hydrogen bonds : angle 5.41399 / 3.61 ( 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 143 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.9269 (t0) cc_final: 0.9050 (t0) REVERT: A 98 MET cc_start: 0.8644 (mmt) cc_final: 0.8254 (mmt) REVERT: A 151 ASN cc_start: 0.9344 (m-40) cc_final: 0.8736 (p0) REVERT: A 552 ILE cc_start: 0.8661 (mt) cc_final: 0.8388 (mp) REVERT: A 630 LYS cc_start: 0.9364 (mmmm) cc_final: 0.9156 (mtpm) REVERT: A 660 GLU cc_start: 0.8496 (mp0) cc_final: 0.8278 (mp0) REVERT: B 78 ASP cc_start: 0.9267 (t0) cc_final: 0.9051 (t0) REVERT: B 98 MET cc_start: 0.8646 (mmt) cc_final: 0.8354 (mmt) REVERT: B 151 ASN cc_start: 0.9326 (m-40) cc_final: 0.8708 (p0) REVERT: B 552 ILE cc_start: 0.8670 (mt) cc_final: 0.8398 (mp) REVERT: B 630 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9110 (mtmm) outliers start: 29 outliers final: 18 residues processed: 136 average time/residue: 0.4455 time to fit residues: 67.7841 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 : 0.500 ------------------------------------------------------------------------------- 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 432 PHE Chi-restraints excluded: chain A residue 453 TYR 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 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 547 THR 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: 0.9980 chunk 129 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 ASN A 274 HIS ** 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 451 ASN ** 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 = 0.3447 r_free = 0.3447 target = 0.086765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.063262 restraints weight = 29800.318| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.29 r_work: 0.2822 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13926 Z= 0.175 Angle : 0.615 9.697 19072 Z= 0.345 Chirality : 0.046 0.240 2088 Planarity : 0.003 0.033 2180 Dihedral : 17.501 162.703 2398 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.54 % Allowed : 13.47 % Favored : 83.98 % 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: -0.06 (0.22), residues: 1486 helix: 1.01 (0.24), residues: 444 sheet: -1.29 (0.30), residues: 246 loop : -0.12 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 56 TYR 0.020 0.001 TYR A 554 PHE 0.015 0.001 PHE B 57 TRP 0.007 0.001 TRP B 623 HIS 0.009 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (13926) covalent geometry : angle 0.61546 / 0.35 (19072) hydrogen bonds : bond 0.03915 / 2.48 ( 554) hydrogen bonds : angle 5.22994 / 3.48 ( 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 138 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8622 (mmt) cc_final: 0.8226 (mmt) REVERT: A 151 ASN cc_start: 0.9325 (m-40) cc_final: 0.8714 (p0) REVERT: A 430 CYS cc_start: 0.7014 (m) cc_final: 0.6240 (m) REVERT: A 548 ARG cc_start: 0.7717 (tpt170) cc_final: 0.7424 (tpt170) REVERT: A 552 ILE cc_start: 0.8641 (mt) cc_final: 0.8359 (mp) REVERT: A 630 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9126 (mtpm) REVERT: A 660 GLU cc_start: 0.8530 (mp0) cc_final: 0.8328 (mp0) REVERT: A 697 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8142 (pp) REVERT: B 98 MET cc_start: 0.8659 (mmt) cc_final: 0.8329 (mmt) REVERT: B 151 ASN cc_start: 0.9320 (m-40) cc_final: 0.8697 (p0) REVERT: B 234 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9001 (pp) REVERT: B 430 CYS cc_start: 0.7034 (m) cc_final: 0.6234 (m) REVERT: B 552 ILE cc_start: 0.8659 (mt) cc_final: 0.8392 (mp) outliers start: 34 outliers final: 22 residues processed: 130 average time/residue: 0.4807 time to fit residues: 68.9816 Evaluate side-chains 122 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 539 CYS 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 234 LEU 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 453 TYR Chi-restraints excluded: chain B residue 539 CYS 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: 0.9990 chunk 77 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 553 HIS A 577 GLN ** B 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.083915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060478 restraints weight = 29850.170| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.24 r_work: 0.2764 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 13926 Z= 0.286 Angle : 0.675 11.619 19072 Z= 0.370 Chirality : 0.047 0.247 2088 Planarity : 0.003 0.051 2180 Dihedral : 17.496 162.566 2398 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.62 % Allowed : 13.40 % Favored : 83.98 % 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: 0.09 (0.22), residues: 1486 helix: 1.14 (0.24), residues: 444 sheet: -1.15 (0.31), residues: 246 loop : -0.04 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 56 TYR 0.018 0.002 TYR B 554 PHE 0.017 0.002 PHE B 591 TRP 0.007 0.001 TRP A 623 HIS 0.009 0.002 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.29 (13926) covalent geometry : angle 0.67489 / 0.37 (19072) hydrogen bonds : bond 0.04036 / 2.58 ( 554) hydrogen bonds : angle 5.21948 / 3.49 ( 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 127 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8679 (mmt) cc_final: 0.8275 (mmt) REVERT: A 151 ASN cc_start: 0.9348 (m-40) cc_final: 0.8739 (p0) REVERT: A 234 LEU cc_start: 0.9458 (mt) cc_final: 0.8964 (pp) REVERT: A 548 ARG cc_start: 0.7853 (tpt170) cc_final: 0.7630 (tpt170) REVERT: A 552 ILE cc_start: 0.8579 (mt) cc_final: 0.8218 (mp) REVERT: A 601 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 697 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8208 (pp) REVERT: B 98 MET cc_start: 0.8691 (mmt) cc_final: 0.8481 (mmt) REVERT: B 234 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.8989 (pp) REVERT: B 418 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9151 (mp0) REVERT: B 552 ILE cc_start: 0.8599 (mt) cc_final: 0.8242 (mp) REVERT: B 601 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8000 (mp0) outliers start: 35 outliers final: 21 residues processed: 118 average time/residue: 0.4599 time to fit residues: 60.1716 Evaluate side-chains 110 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 539 CYS 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 234 LEU 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 453 TYR Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 700 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** B 574 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065013 restraints weight = 29422.030| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.24 r_work: 0.2815 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13926 Z= 0.156 Angle : 0.612 9.730 19072 Z= 0.342 Chirality : 0.046 0.235 2088 Planarity : 0.003 0.056 2180 Dihedral : 17.434 163.104 2398 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.69 % Allowed : 13.85 % 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: 0.26 (0.22), residues: 1486 helix: 1.33 (0.25), residues: 444 sheet: -0.97 (0.33), residues: 230 loop : -0.03 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 56 TYR 0.018 0.001 TYR B 554 PHE 0.014 0.001 PHE A 314 TRP 0.007 0.001 TRP B 482 HIS 0.009 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (13926) covalent geometry : angle 0.61158 / 0.34 (19072) hydrogen bonds : bond 0.03717 / 2.35 ( 554) hydrogen bonds : angle 5.00648 / 3.34 ( 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 140 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8650 (mmt) cc_final: 0.8391 (mmt) REVERT: A 151 ASN cc_start: 0.9320 (m-40) cc_final: 0.8686 (p0) REVERT: A 234 LEU cc_start: 0.9415 (mt) cc_final: 0.8883 (pp) REVERT: A 550 LYS cc_start: 0.8754 (tttp) cc_final: 0.8433 (tttp) REVERT: A 552 ILE cc_start: 0.8581 (mt) cc_final: 0.8099 (mm) REVERT: A 580 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 601 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: B 98 MET cc_start: 0.8681 (mmt) cc_final: 0.8346 (mmt) REVERT: B 234 LEU cc_start: 0.9462 (mt) cc_final: 0.8938 (pp) REVERT: B 552 ILE cc_start: 0.8599 (mt) cc_final: 0.8110 (mm) REVERT: B 580 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8155 (mm-30) REVERT: B 601 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: B 697 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8144 (pp) outliers start: 36 outliers final: 21 residues processed: 131 average time/residue: 0.4326 time to fit residues: 63.2749 Evaluate side-chains 122 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 539 CYS Chi-restraints excluded: chain A residue 601 GLU 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 432 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 145 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 ** 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 = 0.3457 r_free = 0.3457 target = 0.087833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064595 restraints weight = 29134.244| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.23 r_work: 0.2830 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13926 Z= 0.165 Angle : 0.625 11.465 19072 Z= 0.347 Chirality : 0.045 0.233 2088 Planarity : 0.003 0.027 2180 Dihedral : 17.366 162.197 2398 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.69 % Allowed : 14.90 % Favored : 82.41 % 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: 0.33 (0.22), residues: 1486 helix: 1.42 (0.25), residues: 444 sheet: -0.95 (0.33), residues: 230 loop : 0.00 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 56 TYR 0.018 0.001 TYR A 554 PHE 0.015 0.001 PHE B 591 TRP 0.007 0.001 TRP A 528 HIS 0.008 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (13926) covalent geometry : angle 0.62524 / 0.35 (19072) hydrogen bonds : bond 0.03723 / 2.34 ( 554) hydrogen bonds : angle 4.91118 / 3.27 ( 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 139 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8653 (mmt) cc_final: 0.8221 (mmt) REVERT: A 234 LEU cc_start: 0.9418 (mt) cc_final: 0.8880 (pp) REVERT: A 418 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9123 (mp0) REVERT: A 533 MET cc_start: 0.9221 (tpp) cc_final: 0.8774 (tpt) REVERT: A 548 ARG cc_start: 0.7725 (tpt170) cc_final: 0.7512 (tpt170) REVERT: A 550 LYS cc_start: 0.8743 (tttp) cc_final: 0.8411 (tttp) REVERT: A 552 ILE cc_start: 0.8557 (mt) cc_final: 0.8084 (mm) REVERT: A 580 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 601 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: B 98 MET cc_start: 0.8689 (mmt) cc_final: 0.8465 (mmt) REVERT: B 418 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9111 (mp0) REVERT: B 533 MET cc_start: 0.9224 (tpp) cc_final: 0.8768 (tpt) REVERT: B 552 ILE cc_start: 0.8572 (mt) cc_final: 0.8089 (mm) REVERT: B 580 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 601 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: B 697 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8139 (pp) outliers start: 36 outliers final: 23 residues processed: 129 average time/residue: 0.4663 time to fit residues: 67.0497 Evaluate side-chains 124 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 466 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 601 GLU 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 380 PHE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.088010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064396 restraints weight = 29461.484| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.28 r_work: 0.2823 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.3454 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= 0.172 Angle : 0.642 14.192 19072 Z= 0.352 Chirality : 0.046 0.275 2088 Planarity : 0.004 0.106 2180 Dihedral : 17.319 161.859 2398 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.25 % Allowed : 15.72 % 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: 0.38 (0.22), residues: 1486 helix: 1.40 (0.25), residues: 446 sheet: -0.89 (0.33), residues: 230 loop : 0.06 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG A 56 TYR 0.038 0.001 TYR A 108 PHE 0.015 0.001 PHE B 591 TRP 0.005 0.001 TRP B 623 HIS 0.008 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (13926) covalent geometry : angle 0.64235 / 0.35 (19072) hydrogen bonds : bond 0.03649 / 2.30 ( 554) hydrogen bonds : angle 4.83538 / 3.22 ( 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 129 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8660 (mmt) cc_final: 0.8241 (mmt) REVERT: A 418 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9117 (mp0) REVERT: A 533 MET cc_start: 0.9226 (tpp) cc_final: 0.8768 (tpt) REVERT: A 550 LYS cc_start: 0.8723 (tttp) cc_final: 0.8297 (tttp) REVERT: A 552 ILE cc_start: 0.8531 (mt) cc_final: 0.8192 (mp) REVERT: A 580 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 601 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: A 697 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8121 (pp) REVERT: B 98 MET cc_start: 0.8693 (mmt) cc_final: 0.8471 (mmt) REVERT: B 418 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9126 (mp0) REVERT: B 533 MET cc_start: 0.9228 (tpp) cc_final: 0.8775 (tpt) REVERT: B 552 ILE cc_start: 0.8561 (mt) cc_final: 0.8215 (mp) REVERT: B 580 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8068 (mm-30) REVERT: B 601 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 697 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8123 (pp) outliers start: 30 outliers final: 21 residues processed: 123 average time/residue: 0.4714 time to fit residues: 64.9933 Evaluate side-chains 121 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 539 CYS 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 539 CYS 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 149 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.087749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064402 restraints weight = 29387.167| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.24 r_work: 0.2824 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13926 Z= 0.181 Angle : 0.668 15.259 19072 Z= 0.359 Chirality : 0.046 0.252 2088 Planarity : 0.003 0.064 2180 Dihedral : 17.265 161.431 2398 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.32 % Allowed : 15.79 % Favored : 81.89 % 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: 0.43 (0.22), residues: 1486 helix: 1.42 (0.25), residues: 446 sheet: -0.94 (0.33), residues: 234 loop : 0.14 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 56 TYR 0.031 0.001 TYR A 108 PHE 0.016 0.001 PHE A 591 TRP 0.005 0.001 TRP B 623 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (13926) covalent geometry : angle 0.66768 / 0.36 (19072) hydrogen bonds : bond 0.03665 / 2.31 ( 554) hydrogen bonds : angle 4.80166 / 3.19 ( 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 131 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8664 (mmt) cc_final: 0.8348 (mmt) REVERT: A 418 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9114 (mp0) REVERT: A 533 MET cc_start: 0.9227 (tpp) cc_final: 0.8767 (tpt) REVERT: A 552 ILE cc_start: 0.8530 (mt) cc_final: 0.8193 (mp) REVERT: A 580 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8040 (mm-30) REVERT: A 601 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: A 697 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8130 (pp) REVERT: B 24 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8664 (ptp) REVERT: B 98 MET cc_start: 0.8682 (mmt) cc_final: 0.8443 (mmt) REVERT: B 418 GLU cc_start: 0.9459 (mt-10) cc_final: 0.9112 (mp0) REVERT: B 533 MET cc_start: 0.9231 (tpp) cc_final: 0.8775 (tpt) REVERT: B 552 ILE cc_start: 0.8541 (mt) cc_final: 0.8151 (mp) REVERT: B 580 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8033 (mm-30) REVERT: B 601 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: B 697 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8123 (pp) outliers start: 31 outliers final: 17 residues processed: 123 average time/residue: 0.4980 time to fit residues: 68.8050 Evaluate side-chains 117 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 396 ILE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 601 GLU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 24 MET 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 432 PHE Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 539 CYS 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 145 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.088348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.064876 restraints weight = 29508.083| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.27 r_work: 0.2835 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13926 Z= 0.166 Angle : 0.678 14.444 19072 Z= 0.364 Chirality : 0.046 0.253 2088 Planarity : 0.004 0.093 2180 Dihedral : 17.131 161.168 2398 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.02 % Allowed : 16.54 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.46 (0.22), residues: 1486 helix: 1.42 (0.25), residues: 446 sheet: -0.86 (0.33), residues: 234 loop : 0.16 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 56 TYR 0.032 0.001 TYR A 108 PHE 0.015 0.001 PHE A 591 TRP 0.005 0.001 TRP B 623 HIS 0.007 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (13926) covalent geometry : angle 0.67793 / 0.36 (19072) hydrogen bonds : bond 0.03602 / 2.25 ( 554) hydrogen bonds : angle 4.75424 / 3.16 ( 1540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3150.24 seconds wall clock time: 54 minutes 58.49 seconds (3298.49 seconds total)