Starting phenix.real_space_refine on Thu Sep 18 04:03:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhl_61486/09_2025/9jhl_61486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhl_61486/09_2025/9jhl_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_61486/09_2025/9jhl_61486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhl_61486/09_2025/9jhl_61486.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhl_61486/09_2025/9jhl_61486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhl_61486/09_2025/9jhl_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-2.0-5805/lib/python3.9/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: 5.46, 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: 1.01 Conformation dependent library (CDL) restraints added in 496.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.57 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: 2.64 Time building geometry restraints manager: 1.35 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=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.82e+00 bond pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.23e-02 6.61e+03 6.46e+00 bond pdb=" CG1 ILE A 678 " pdb=" CD1 ILE A 678 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.24e+00 bond pdb=" CG1 ILE B 678 " pdb=" CD1 ILE B 678 " ideal model delta sigma weight residual 1.513 1.416 0.097 3.90e-02 6.57e+02 6.15e+00 bond pdb=" C3' DG D 15 " pdb=" O3' DG D 15 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.22e+00 ... (remaining 13921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 18431 2.18 - 4.37: 558 4.37 - 6.55: 63 6.55 - 8.74: 16 8.74 - 10.92: 4 Bond angle restraints: 19072 Sorted by residual: angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.82 128.90 -8.08 1.50e+00 4.44e-01 2.90e+01 angle pdb=" C LYS B 63 " pdb=" N ASP B 64 " pdb=" CA ASP B 64 " ideal model delta sigma weight residual 120.82 128.86 -8.04 1.50e+00 4.44e-01 2.88e+01 angle pdb=" N LYS A 63 " pdb=" CA LYS A 63 " pdb=" C LYS A 63 " ideal model delta sigma weight residual 110.14 102.32 7.82 1.47e+00 4.63e-01 2.83e+01 angle pdb=" N LYS B 63 " pdb=" CA LYS B 63 " pdb=" C LYS B 63 " ideal model delta sigma weight residual 110.14 102.35 7.79 1.47e+00 4.63e-01 2.81e+01 angle pdb=" C ILE A 471 " pdb=" N GLU A 472 " pdb=" CA GLU A 472 " ideal model delta sigma weight residual 120.90 126.59 -5.69 1.41e+00 5.03e-01 1.63e+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: 1525 0.056 - 0.111: 461 0.111 - 0.167: 84 0.167 - 0.223: 13 0.223 - 0.278: 5 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: 2.420 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 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: 0.7169 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= 0.308 Angle : 0.891 10.920 19072 Z= 0.493 Chirality : 0.056 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 aren 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 covalent geometry : bond 0.00758 (13926) covalent geometry : angle 0.89141 (19072) hydrogen bonds : bond 0.19805 ( 554) hydrogen bonds : angle 8.73998 ( 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 : 0.533 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: 0.6979 time to fit residues: 191.7015 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 : 0.523 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 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 409 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 612 HIS B 28 GLN B 55 ASN B 136 ASN B 265 ASN ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN B 409 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 612 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.065856 restraints weight = 29838.459| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.24 r_work: 0.2885 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2436 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= 0.174 Angle : 0.620 5.988 19072 Z= 0.342 Chirality : 0.045 0.170 2088 Planarity : 0.004 0.039 2180 Dihedral : 17.815 158.724 2402 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.87 % Allowed : 10.93 % Favored : 87.20 % 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 aren not related in a simple way. whole: -1.21 (0.20), residues: 1486 helix: -0.45 (0.22), residues: 444 sheet: -1.17 (0.28), residues: 288 loop : -0.74 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 743 TYR 0.019 0.001 TYR B 511 PHE 0.011 0.001 PHE A 154 TRP 0.020 0.002 TRP B 623 HIS 0.013 0.002 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00387 (13926) covalent geometry : angle 0.61967 (19072) hydrogen bonds : bond 0.04487 ( 554) hydrogen bonds : angle 5.61694 ( 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 170 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8612 (mmt) cc_final: 0.8337 (mmt) REVERT: A 151 ASN cc_start: 0.9258 (m-40) cc_final: 0.8687 (p0) REVERT: A 193 LYS cc_start: 0.9339 (ttmm) cc_final: 0.8990 (mmmm) REVERT: A 250 PHE cc_start: 0.9231 (m-10) cc_final: 0.8968 (m-80) REVERT: A 365 ILE cc_start: 0.9430 (tp) cc_final: 0.9190 (tp) REVERT: A 418 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9139 (mp0) REVERT: A 505 ASP cc_start: 0.9008 (p0) cc_final: 0.8799 (p0) REVERT: A 548 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7129 (ttm170) REVERT: A 552 ILE cc_start: 0.8799 (mt) cc_final: 0.8523 (mp) REVERT: A 700 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9096 (tm) REVERT: B 78 ASP cc_start: 0.9188 (t0) cc_final: 0.8930 (t0) REVERT: B 98 MET cc_start: 0.8597 (mmt) cc_final: 0.8262 (mmt) REVERT: B 151 ASN cc_start: 0.9241 (m-40) cc_final: 0.8657 (p0) REVERT: B 193 LYS cc_start: 0.9344 (ttmm) cc_final: 0.8980 (mmmm) REVERT: B 365 ILE cc_start: 0.9427 (tp) cc_final: 0.9166 (tp) REVERT: B 505 ASP cc_start: 0.8981 (p0) cc_final: 0.8767 (p0) REVERT: B 548 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7126 (ttm170) REVERT: B 552 ILE cc_start: 0.8798 (mt) cc_final: 0.8528 (mp) REVERT: B 700 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9103 (tm) outliers start: 25 outliers final: 6 residues processed: 165 average time/residue: 0.6193 time to fit residues: 111.7623 Evaluate side-chains 122 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 700 LEU 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 700 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 274 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 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 = 0.3470 r_free = 0.3470 target = 0.089292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.065070 restraints weight = 29606.755| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.39 r_work: 0.2817 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13926 Z= 0.185 Angle : 0.595 9.634 19072 Z= 0.326 Chirality : 0.045 0.162 2088 Planarity : 0.003 0.028 2180 Dihedral : 17.348 155.529 2398 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.84 % Allowed : 12.20 % Favored : 84.96 % 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 aren not related in a simple way. whole: -0.46 (0.21), residues: 1486 helix: 0.47 (0.23), residues: 444 sheet: -1.19 (0.29), residues: 254 loop : -0.33 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 743 TYR 0.015 0.001 TYR A 306 PHE 0.013 0.002 PHE B 591 TRP 0.012 0.002 TRP B 623 HIS 0.005 0.001 HIS B 513 Details of bonding type rmsd covalent geometry : bond 0.00420 (13926) covalent geometry : angle 0.59536 (19072) hydrogen bonds : bond 0.03870 ( 554) hydrogen bonds : angle 5.17801 ( 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 164 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8614 (mmt) cc_final: 0.8291 (mmt) REVERT: A 151 ASN cc_start: 0.9312 (m-40) cc_final: 0.8704 (p0) REVERT: A 365 ILE cc_start: 0.9476 (tp) cc_final: 0.9274 (tp) REVERT: A 418 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9110 (mp0) REVERT: A 430 CYS cc_start: 0.7164 (m) cc_final: 0.6228 (m) REVERT: A 548 ARG cc_start: 0.7811 (ttm170) cc_final: 0.7379 (ttm110) REVERT: A 552 ILE cc_start: 0.8684 (mt) cc_final: 0.8402 (mp) REVERT: A 630 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9096 (mtmm) REVERT: B 98 MET cc_start: 0.8624 (mmt) cc_final: 0.8290 (mmm) REVERT: B 151 ASN cc_start: 0.9297 (m-40) cc_final: 0.8681 (p0) REVERT: B 266 LYS cc_start: 0.9496 (mptt) cc_final: 0.9226 (pmtt) REVERT: B 365 ILE cc_start: 0.9474 (tp) cc_final: 0.9259 (tp) REVERT: B 430 CYS cc_start: 0.7022 (m) cc_final: 0.6134 (m) REVERT: B 548 ARG cc_start: 0.7825 (ttm170) cc_final: 0.7393 (ttm110) REVERT: B 552 ILE cc_start: 0.8686 (mt) cc_final: 0.8402 (mp) outliers start: 38 outliers final: 14 residues processed: 151 average time/residue: 0.5234 time to fit residues: 87.2851 Evaluate side-chains 119 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN B 39 ASN B 274 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.086892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063447 restraints weight = 29506.387| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.29 r_work: 0.2801 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13926 Z= 0.218 Angle : 0.600 7.005 19072 Z= 0.329 Chirality : 0.046 0.230 2088 Planarity : 0.003 0.043 2180 Dihedral : 17.334 154.932 2398 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.77 % Allowed : 12.95 % Favored : 84.28 % 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 aren not related in a simple way. whole: 0.04 (0.22), residues: 1486 helix: 1.01 (0.24), residues: 446 sheet: -1.03 (0.30), residues: 250 loop : -0.07 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 56 TYR 0.015 0.001 TYR B 306 PHE 0.015 0.001 PHE B 591 TRP 0.014 0.002 TRP A 482 HIS 0.005 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00499 (13926) covalent geometry : angle 0.60018 (19072) hydrogen bonds : bond 0.03722 ( 554) hydrogen bonds : angle 4.99986 ( 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 153 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.531 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: 0.8620 (mmt) cc_final: 0.8363 (mmt) REVERT: A 151 ASN cc_start: 0.9317 (m-40) cc_final: 0.8691 (p0) REVERT: A 234 LEU cc_start: 0.9462 (mt) cc_final: 0.8932 (pp) REVERT: A 418 GLU cc_start: 0.9469 (mt-10) cc_final: 0.9127 (mp0) REVERT: A 533 MET cc_start: 0.9226 (tpp) cc_final: 0.8734 (tpt) REVERT: A 548 ARG cc_start: 0.7877 (ttm170) cc_final: 0.7517 (ttm110) REVERT: A 552 ILE cc_start: 0.8590 (mt) cc_final: 0.8338 (mp) REVERT: B 78 ASP cc_start: 0.9182 (t0) cc_final: 0.8980 (t0) REVERT: B 98 MET cc_start: 0.8678 (mmt) cc_final: 0.8333 (mmt) REVERT: B 234 LEU cc_start: 0.9478 (mt) cc_final: 0.8996 (pp) REVERT: B 418 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9138 (mp0) REVERT: B 548 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7504 (ttm110) REVERT: B 552 ILE cc_start: 0.8597 (mt) cc_final: 0.8328 (mp) outliers start: 37 outliers final: 17 residues processed: 143 average time/residue: 0.5141 time to fit residues: 81.5340 Evaluate side-chains 113 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 271 TYR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 432 PHE 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: 3.9990 chunk 50 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 451 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.064619 restraints weight = 29719.796| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.29 r_work: 0.2822 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13926 Z= 0.177 Angle : 0.587 10.523 19072 Z= 0.322 Chirality : 0.045 0.208 2088 Planarity : 0.003 0.039 2180 Dihedral : 17.289 153.458 2398 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.77 % Allowed : 13.85 % Favored : 83.38 % 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 aren not related in a simple way. whole: 0.31 (0.22), residues: 1486 helix: 1.36 (0.25), residues: 446 sheet: -1.01 (0.31), residues: 246 loop : 0.05 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.014 0.001 TYR B 511 PHE 0.015 0.001 PHE B 250 TRP 0.008 0.001 TRP A 482 HIS 0.008 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00403 (13926) covalent geometry : angle 0.58650 (19072) hydrogen bonds : bond 0.03497 ( 554) hydrogen bonds : angle 4.83709 ( 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 146 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.500 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: 0.8602 (mmt) cc_final: 0.8253 (mmt) REVERT: A 353 MET cc_start: 0.9043 (mmm) cc_final: 0.8828 (mmm) REVERT: A 418 GLU cc_start: 0.9464 (mt-10) cc_final: 0.9103 (mp0) REVERT: A 548 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7565 (ttm110) REVERT: A 552 ILE cc_start: 0.8538 (mt) cc_final: 0.8264 (mp) REVERT: A 584 THR cc_start: 0.8828 (p) cc_final: 0.8609 (t) REVERT: A 601 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: B 98 MET cc_start: 0.8642 (mmt) cc_final: 0.8381 (mmt) REVERT: B 353 MET cc_start: 0.9037 (mmm) cc_final: 0.8823 (mmm) REVERT: B 548 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7534 (ttm110) REVERT: B 552 ILE cc_start: 0.8540 (mt) cc_final: 0.8262 (mp) REVERT: B 584 THR cc_start: 0.8835 (p) cc_final: 0.8612 (t) outliers start: 37 outliers final: 21 residues processed: 137 average time/residue: 0.5432 time to fit residues: 82.8981 Evaluate side-chains 127 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 62 ILE 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 337 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 PHE 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 62 ILE 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 396 ILE Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 453 TYR 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: 3.9990 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 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: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 274 HIS ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.056907 restraints weight = 30112.950| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.21 r_work: 0.2682 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.084 13926 Z= 0.422 Angle : 0.724 10.671 19072 Z= 0.388 Chirality : 0.052 0.203 2088 Planarity : 0.004 0.055 2180 Dihedral : 17.677 156.241 2398 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.22 % Allowed : 13.77 % Favored : 83.01 % 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 aren not related in a simple way. whole: 0.16 (0.22), residues: 1486 helix: 1.12 (0.24), residues: 446 sheet: -1.16 (0.30), residues: 262 loop : 0.11 (0.24), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 56 TYR 0.019 0.002 TYR B 122 PHE 0.022 0.002 PHE A 591 TRP 0.008 0.002 TRP B 623 HIS 0.009 0.002 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00969 (13926) covalent geometry : angle 0.72415 (19072) hydrogen bonds : bond 0.04141 ( 554) hydrogen bonds : angle 5.22683 ( 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 148 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8701 (mmt) cc_final: 0.8435 (mmt) REVERT: A 256 ASN cc_start: 0.9390 (m110) cc_final: 0.9173 (m110) REVERT: A 353 MET cc_start: 0.9053 (mmm) cc_final: 0.8838 (mmm) REVERT: A 418 GLU cc_start: 0.9454 (mt-10) cc_final: 0.9166 (mp0) REVERT: A 548 ARG cc_start: 0.8055 (ttm170) cc_final: 0.7517 (ttm110) REVERT: A 552 ILE cc_start: 0.8555 (mt) cc_final: 0.8173 (mp) REVERT: A 601 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 697 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 353 MET cc_start: 0.9047 (mmm) cc_final: 0.8833 (mmm) REVERT: B 418 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9181 (mp0) REVERT: B 548 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7491 (ttm110) REVERT: B 552 ILE cc_start: 0.8558 (mt) cc_final: 0.8169 (mp) REVERT: B 601 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: B 697 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8359 (pp) outliers start: 43 outliers final: 13 residues processed: 130 average time/residue: 0.6331 time to fit residues: 90.7086 Evaluate side-chains 109 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 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 179 SER 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 601 GLU Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** A 451 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.085208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062428 restraints weight = 29723.869| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.14 r_work: 0.2829 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13926 Z= 0.162 Angle : 0.611 11.451 19072 Z= 0.333 Chirality : 0.045 0.202 2088 Planarity : 0.004 0.057 2180 Dihedral : 17.471 154.215 2398 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.10 % Allowed : 16.17 % Favored : 81.74 % 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 aren not related in a simple way. whole: 0.45 (0.22), residues: 1486 helix: 1.53 (0.25), residues: 446 sheet: -0.95 (0.31), residues: 266 loop : 0.15 (0.24), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 743 TYR 0.013 0.001 TYR B 511 PHE 0.015 0.001 PHE A 591 TRP 0.008 0.001 TRP A 482 HIS 0.011 0.002 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00366 (13926) covalent geometry : angle 0.61118 (19072) hydrogen bonds : bond 0.03493 ( 554) hydrogen bonds : angle 4.80941 ( 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 134 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8670 (mmt) cc_final: 0.8304 (mmt) REVERT: A 256 ASN cc_start: 0.9353 (m110) cc_final: 0.9129 (m110) REVERT: A 353 MET cc_start: 0.8953 (mmm) cc_final: 0.8699 (mmm) REVERT: A 418 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9130 (mm-30) REVERT: A 552 ILE cc_start: 0.8548 (mt) cc_final: 0.8304 (mp) REVERT: A 601 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: B 98 MET cc_start: 0.8795 (mmt) cc_final: 0.8550 (mmt) REVERT: B 353 MET cc_start: 0.8958 (mmm) cc_final: 0.8706 (mmm) REVERT: B 418 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9146 (mp0) REVERT: B 552 ILE cc_start: 0.8544 (mt) cc_final: 0.8164 (mp) REVERT: B 601 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7963 (mp0) outliers start: 28 outliers final: 15 residues processed: 127 average time/residue: 0.6487 time to fit residues: 90.3533 Evaluate side-chains 118 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 337 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 PHE 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 260 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 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: 0.6980 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** 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 = 0.3425 r_free = 0.3425 target = 0.085989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.062823 restraints weight = 29209.516| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.21 r_work: 0.2784 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13926 Z= 0.199 Angle : 0.623 11.426 19072 Z= 0.336 Chirality : 0.045 0.198 2088 Planarity : 0.003 0.037 2180 Dihedral : 17.352 153.154 2398 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.57 % Allowed : 17.89 % Favored : 80.54 % 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 aren not related in a simple way. whole: 0.62 (0.22), residues: 1486 helix: 1.58 (0.25), residues: 446 sheet: -0.81 (0.33), residues: 242 loop : 0.27 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 56 TYR 0.013 0.001 TYR A 306 PHE 0.017 0.001 PHE A 591 TRP 0.006 0.001 TRP A 482 HIS 0.008 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00458 (13926) covalent geometry : angle 0.62298 (19072) hydrogen bonds : bond 0.03441 ( 554) hydrogen bonds : angle 4.74516 ( 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 119 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.536 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: 0.8609 (mmt) cc_final: 0.8339 (mmt) REVERT: A 353 MET cc_start: 0.8891 (mmm) cc_final: 0.8585 (mmm) REVERT: A 418 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9138 (mp0) REVERT: A 552 ILE cc_start: 0.8487 (mt) cc_final: 0.8102 (mp) REVERT: B 98 MET cc_start: 0.8746 (mmt) cc_final: 0.8489 (mmt) REVERT: B 353 MET cc_start: 0.8886 (mmm) cc_final: 0.8578 (mmm) REVERT: B 418 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9146 (mm-30) REVERT: B 552 ILE cc_start: 0.8485 (mt) cc_final: 0.8099 (mp) REVERT: B 601 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8006 (mp0) outliers start: 21 outliers final: 14 residues processed: 112 average time/residue: 0.6368 time to fit residues: 78.7097 Evaluate side-chains 110 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 337 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 179 SER 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 601 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 63 optimal weight: 0.0010 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** 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 = 0.3478 r_free = 0.3478 target = 0.088309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065164 restraints weight = 29424.957| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.20 r_work: 0.2861 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3888 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= 0.152 Angle : 0.623 14.022 19072 Z= 0.335 Chirality : 0.044 0.196 2088 Planarity : 0.003 0.032 2180 Dihedral : 17.262 151.385 2398 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.35 % Allowed : 18.34 % Favored : 80.31 % 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 aren not related in a simple way. whole: 0.63 (0.23), residues: 1486 helix: 1.60 (0.25), residues: 452 sheet: -0.68 (0.33), residues: 246 loop : 0.21 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 56 TYR 0.014 0.001 TYR A 306 PHE 0.021 0.001 PHE B 250 TRP 0.007 0.001 TRP A 482 HIS 0.012 0.002 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00349 (13926) covalent geometry : angle 0.62335 (19072) hydrogen bonds : bond 0.03266 ( 554) hydrogen bonds : angle 4.62559 ( 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 133 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.534 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: 0.8619 (mmt) cc_final: 0.8227 (mmt) REVERT: A 353 MET cc_start: 0.8905 (mmm) cc_final: 0.8636 (mmm) REVERT: A 418 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9098 (mp0) REVERT: A 552 ILE cc_start: 0.8561 (mt) cc_final: 0.8186 (mp) REVERT: B 98 MET cc_start: 0.8771 (mmt) cc_final: 0.8498 (mmt) REVERT: B 353 MET cc_start: 0.8904 (mmm) cc_final: 0.8635 (mmm) REVERT: B 418 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9122 (mm-30) REVERT: B 552 ILE cc_start: 0.8526 (mt) cc_final: 0.8148 (mp) outliers start: 18 outliers final: 12 residues processed: 128 average time/residue: 0.5870 time to fit residues: 83.4014 Evaluate side-chains 119 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 260 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 PHE 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 337 VAL Chi-restraints excluded: chain B residue 432 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 142 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 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 = 0.087696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065128 restraints weight = 29520.161| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.15 r_work: 0.2878 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13926 Z= 0.148 Angle : 0.626 12.732 19072 Z= 0.337 Chirality : 0.044 0.193 2088 Planarity : 0.004 0.106 2180 Dihedral : 17.176 149.534 2398 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.12 % Allowed : 19.69 % Favored : 79.19 % 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 aren not related in a simple way. whole: 0.70 (0.23), residues: 1486 helix: 1.62 (0.25), residues: 452 sheet: -0.61 (0.33), residues: 246 loop : 0.26 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG A 56 TYR 0.013 0.001 TYR B 511 PHE 0.017 0.001 PHE A 250 TRP 0.007 0.001 TRP A 482 HIS 0.010 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00340 (13926) covalent geometry : angle 0.62637 (19072) hydrogen bonds : bond 0.03199 ( 554) hydrogen bonds : angle 4.53778 ( 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 127 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.529 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: 0.8586 (mmt) cc_final: 0.8191 (mmt) REVERT: A 353 MET cc_start: 0.8882 (mmm) cc_final: 0.8514 (mmm) REVERT: A 418 GLU cc_start: 0.9413 (mt-10) cc_final: 0.9119 (mm-30) REVERT: A 552 ILE cc_start: 0.8507 (mt) cc_final: 0.8137 (mp) REVERT: B 24 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8476 (ptp) REVERT: B 98 MET cc_start: 0.8752 (mmt) cc_final: 0.8454 (mmt) REVERT: B 302 MET cc_start: 0.9018 (mtp) cc_final: 0.8811 (mtm) REVERT: B 353 MET cc_start: 0.8880 (mmm) cc_final: 0.8511 (mmm) REVERT: B 418 GLU cc_start: 0.9411 (mt-10) cc_final: 0.9125 (mm-30) REVERT: B 552 ILE cc_start: 0.8494 (mt) cc_final: 0.8119 (mp) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.6085 time to fit residues: 82.1188 Evaluate side-chains 113 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 432 PHE 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 260 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 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: 0.8980 chunk 118 optimal weight: 0.1980 chunk 117 optimal weight: 0.0470 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 102 optimal weight: 0.0670 chunk 121 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066517 restraints weight = 30148.056| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.23 r_work: 0.2904 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13926 Z= 0.139 Angle : 0.639 15.039 19072 Z= 0.343 Chirality : 0.044 0.193 2088 Planarity : 0.004 0.080 2180 Dihedral : 17.124 148.631 2398 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.05 % Allowed : 20.36 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.22), residues: 1486 helix: 1.67 (0.25), residues: 452 sheet: -0.60 (0.32), residues: 258 loop : 0.27 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 56 TYR 0.013 0.001 TYR B 511 PHE 0.028 0.001 PHE B 250 TRP 0.008 0.001 TRP A 482 HIS 0.011 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00320 (13926) covalent geometry : angle 0.63879 (19072) hydrogen bonds : bond 0.03165 ( 554) hydrogen bonds : angle 4.49165 ( 1540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3778.07 seconds wall clock time: 65 minutes 47.15 seconds (3947.15 seconds total)