Starting phenix.real_space_refine on Thu Aug 6 06:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhn_61488/08_2026/9jhn_61488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhn_61488/08_2026/9jhn_61488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jhn_61488/08_2026/9jhn_61488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhn_61488/08_2026/9jhn_61488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jhn_61488/08_2026/9jhn_61488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhn_61488/08_2026/9jhn_61488.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 70 5.49 5 S 40 5.16 5 C 8488 2.51 5 N 2230 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13512 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" 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: 6.21, per 1000 atoms: 0.46 Number of scatterers: 13512 At special positions: 0 Unit cell: (89.38, 118.9, 103.32, 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: 1.06 Conformation dependent library (CDL) restraints added in 538.9 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 28 sheets defined 31.4% alpha, 17.2% beta 22 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 43 through 54 Processing helix chain 'A' and resid 97 through 115 removed outlier: 4.078A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.745A pdb=" N MET A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 253 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 removed outlier: 3.662A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.585A pdb=" N LEU A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) 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 452 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.106A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.994A 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 630 Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.567A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) 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: 4.078A pdb=" N LYS B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.744A pdb=" N MET B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 253 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 removed outlier: 3.662A pdb=" N LYS B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.586A pdb=" N LEU B 339 " --> pdb=" O ASP B 336 " (cutoff:3.500A) 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 452 Processing helix chain 'B' and resid 474 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.105A pdb=" N TYR B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 3.994A 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 630 Processing helix chain 'B' and resid 698 through 711 removed outlier: 3.566A pdb=" N ALA B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.697A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.347A pdb=" N GLN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 62 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 125 through 127 removed outlier: 3.732A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.830A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE A 259 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL A 219 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 215 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 214 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.679A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP A 562 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 567 " --> pdb=" O ASP A 562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 358 through 359 removed outlier: 4.807A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 529 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.775A pdb=" N VAL A 378 " --> pdb=" O GLU A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 382 through 385 removed outlier: 5.976A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 166 removed outlier: 4.697A pdb=" N VAL B 172 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.346A pdb=" N GLN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AC1, first strand: chain 'B' and resid 117 through 118 Processing sheet with id=AC2, first strand: chain 'B' and resid 125 through 127 removed outlier: 3.731A pdb=" N LEU B 134 " --> pdb=" O ARG B 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AC4, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.829A pdb=" N TYR B 271 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 260 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 259 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL B 219 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN B 261 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 215 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 214 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.680A pdb=" N ILE B 637 " --> pdb=" O SER B 693 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 609 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 638 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 611 " --> pdb=" O ILE B 638 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 640 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG B 613 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N CYS B 539 " --> pdb=" O VAL B 610 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N HIS B 612 " --> pdb=" O CYS B 539 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 541 " --> pdb=" O HIS B 612 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 614 " --> pdb=" O VAL B 541 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 543 " --> pdb=" O ALA B 614 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 562 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 567 " --> pdb=" O ASP B 562 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 4.806A pdb=" N LEU B 352 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 529 " --> pdb=" O MET B 353 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.774A pdb=" N VAL B 378 " --> pdb=" O GLU B 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 382 through 385 removed outlier: 5.976A pdb=" N VAL B 382 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 435 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 384 " --> pdb=" O TYR B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AD1, first strand: chain 'B' and resid 462 through 463 442 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.47 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: 2891 1.33 - 1.45: 3309 1.45 - 1.57: 7520 1.57 - 1.69: 136 1.69 - 1.81: 70 Bond restraints: 13926 Sorted by residual: bond pdb=" C3' DA D 7 " pdb=" O3' DA D 7 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C3' DA C 7 " pdb=" O3' DA C 7 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" C3' DG D 8 " pdb=" O3' DG D 8 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.62e+01 bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" C3' DG D 5 " pdb=" O3' DG D 5 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.37e+01 ... (remaining 13921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 17838 1.87 - 3.73: 1077 3.73 - 5.60: 113 5.60 - 7.47: 31 7.47 - 9.34: 13 Bond angle restraints: 19072 Sorted by residual: angle pdb=" O4' DA C 17 " pdb=" C1' DA C 17 " pdb=" N9 DA C 17 " ideal model delta sigma weight residual 108.00 112.13 -4.13 7.00e-01 2.04e+00 3.49e+01 angle pdb=" O4' DA D 17 " pdb=" C1' DA D 17 " pdb=" N9 DA D 17 " ideal model delta sigma weight residual 108.00 112.10 -4.10 7.00e-01 2.04e+00 3.43e+01 angle pdb=" O4' DG D 4 " pdb=" C4' DG D 4 " pdb=" C3' DG D 4 " ideal model delta sigma weight residual 106.00 102.55 3.45 6.00e-01 2.78e+00 3.30e+01 angle pdb=" O4' DG C 4 " pdb=" C4' DG C 4 " pdb=" C3' DG C 4 " ideal model delta sigma weight residual 106.00 102.56 3.44 6.00e-01 2.78e+00 3.29e+01 angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.54 127.93 -7.39 1.35e+00 5.49e-01 3.00e+01 ... (remaining 19067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 7895 29.81 - 59.61: 352 59.61 - 89.42: 15 89.42 - 119.22: 0 119.22 - 149.03: 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 -143.69 -36.31 0 5.00e+00 4.00e-02 5.27e+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 -143.75 -36.25 0 5.00e+00 4.00e-02 5.26e+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 -148.14 -31.86 0 5.00e+00 4.00e-02 4.06e+01 ... (remaining 8261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1670 0.075 - 0.150: 366 0.150 - 0.225: 42 0.225 - 0.300: 6 0.300 - 0.375: 4 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 2.27 0.37 2.00e-01 2.50e+01 3.51e+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 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE A 596 " pdb=" CA ILE A 596 " pdb=" CG1 ILE A 596 " pdb=" CG2 ILE A 596 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2085 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " -0.017 2.00e-02 2.50e+03 1.36e-02 4.60e+00 pdb=" CG TRP B 623 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " 0.017 2.00e-02 2.50e+03 1.33e-02 4.42e+00 pdb=" CG TRP A 623 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " 0.005 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 " -0.014 2.00e-02 2.50e+03 1.68e-02 4.24e+00 pdb=" CG HIS B 513 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS B 513 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS B 513 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 HIS B 513 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS B 513 " -0.004 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 84 2.50 - 3.10: 9004 3.10 - 3.70: 21376 3.70 - 4.30: 32705 4.30 - 4.90: 52409 Nonbonded interactions: 115578 Sorted by model distance: nonbonded pdb=" OP2 DT D 1 " pdb="MN MN D 801 " model vdw 1.895 2.320 nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.895 2.320 nonbonded pdb=" OP1 DT D 1 " pdb="MN MN D 801 " model vdw 1.923 2.320 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 1.923 2.320 nonbonded pdb=" NZ LYS B 54 " pdb=" CD1 LEU B 79 " model vdw 1.944 3.540 ... (remaining 115573 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: 2.740 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.540 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 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 : 0.010 0.093 13926 Z= 0.552 Angle : 0.990 9.336 19072 Z= 0.629 Chirality : 0.064 0.375 2088 Planarity : 0.006 0.043 2180 Dihedral : 14.778 149.028 5476 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.15 % Allowed : 1.95 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.07 (0.18), residues: 1486 helix: -2.44 (0.18), residues: 444 sheet: -2.15 (0.24), residues: 342 loop : -1.52 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 721 TYR 0.027 0.003 TYR A 511 PHE 0.025 0.004 PHE B 591 TRP 0.033 0.006 TRP B 623 HIS 0.020 0.004 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00978 / 0.55 (13926) covalent geometry : angle 0.98992 / 0.63 (19072) hydrogen bonds : bond 0.20092 / 12.98 ( 492) hydrogen bonds : angle 9.18993 / 6.47 ( 1336) *********************** 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 202 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.542 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: 2 outliers final: 2 residues processed: 202 average time/residue: 0.4897 time to fit residues: 108.9142 Evaluate side-chains 89 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain B residue 432 PHE 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: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS A 298 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN B 274 HIS B 298 GLN ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.072146 restraints weight = 34000.165| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.68 r_work: 0.3120 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1873 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= 0.173 Angle : 0.706 8.288 19072 Z= 0.390 Chirality : 0.047 0.237 2088 Planarity : 0.004 0.035 2180 Dihedral : 17.524 154.256 2402 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.17 % Allowed : 8.23 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.20), residues: 1486 helix: -0.79 (0.22), residues: 438 sheet: -1.82 (0.26), residues: 322 loop : -0.91 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 158 TYR 0.019 0.002 TYR B 306 PHE 0.034 0.002 PHE B 250 TRP 0.016 0.002 TRP B 623 HIS 0.006 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (13926) covalent geometry : angle 0.70586 / 0.39 (19072) hydrogen bonds : bond 0.05222 / 3.20 ( 492) hydrogen bonds : angle 6.30039 / 4.42 ( 1336) *********************** 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 148 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.333 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 81 PHE cc_start: 0.8160 (p90) cc_final: 0.7890 (p90) REVERT: A 132 GLU cc_start: 0.7906 (pm20) cc_final: 0.7669 (pm20) REVERT: A 142 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 217 GLU cc_start: 0.8932 (tp30) cc_final: 0.8481 (mp0) REVERT: A 415 TYR cc_start: 0.8751 (m-80) cc_final: 0.8457 (m-10) REVERT: A 600 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8692 (mm-30) REVERT: B 81 PHE cc_start: 0.8165 (p90) cc_final: 0.7885 (p90) REVERT: B 132 GLU cc_start: 0.7908 (pm20) cc_final: 0.7663 (pm20) REVERT: B 142 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8207 (tm-30) REVERT: B 217 GLU cc_start: 0.8922 (tp30) cc_final: 0.8467 (mp0) REVERT: B 399 ILE cc_start: 0.9483 (mt) cc_final: 0.9256 (pp) REVERT: B 600 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8691 (mm-30) outliers start: 29 outliers final: 13 residues processed: 142 average time/residue: 0.3977 time to fit residues: 63.6490 Evaluate side-chains 97 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 432 PHE Chi-restraints excluded: chain B residue 547 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.094352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071789 restraints weight = 34578.652| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.65 r_work: 0.3119 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13926 Z= 0.171 Angle : 0.640 6.947 19072 Z= 0.355 Chirality : 0.046 0.231 2088 Planarity : 0.003 0.027 2180 Dihedral : 17.464 153.945 2402 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.77 % Allowed : 9.28 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.21), residues: 1486 helix: -0.09 (0.23), residues: 452 sheet: -1.74 (0.26), residues: 330 loop : -0.65 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 721 TYR 0.016 0.001 TYR A 306 PHE 0.016 0.002 PHE B 250 TRP 0.009 0.001 TRP B 623 HIS 0.006 0.001 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (13926) covalent geometry : angle 0.63974 / 0.36 (19072) hydrogen bonds : bond 0.04236 / 2.61 ( 492) hydrogen bonds : angle 5.68016 / 3.94 ( 1336) *********************** 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 128 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8566 (mmtp) REVERT: A 81 PHE cc_start: 0.8256 (p90) cc_final: 0.7911 (p90) REVERT: A 132 GLU cc_start: 0.7887 (pm20) cc_final: 0.7595 (pm20) REVERT: A 142 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 217 GLU cc_start: 0.8923 (tp30) cc_final: 0.8476 (mp0) REVERT: A 415 TYR cc_start: 0.8760 (m-80) cc_final: 0.8522 (m-10) REVERT: B 58 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8567 (mmtp) REVERT: B 81 PHE cc_start: 0.8243 (p90) cc_final: 0.7872 (p90) REVERT: B 132 GLU cc_start: 0.7905 (pm20) cc_final: 0.7606 (pm20) REVERT: B 142 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8154 (tm-30) REVERT: B 217 GLU cc_start: 0.8921 (tp30) cc_final: 0.8409 (mp0) outliers start: 37 outliers final: 19 residues processed: 119 average time/residue: 0.4007 time to fit residues: 54.0230 Evaluate side-chains 96 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 378 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 368 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 = 0.3683 r_free = 0.3683 target = 0.091426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.068907 restraints weight = 34890.085| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.61 r_work: 0.3056 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13926 Z= 0.277 Angle : 0.692 7.139 19072 Z= 0.379 Chirality : 0.048 0.252 2088 Planarity : 0.003 0.023 2180 Dihedral : 17.359 153.395 2402 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.99 % Allowed : 9.81 % 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 are not related in a simple way. whole: -0.97 (0.21), residues: 1486 helix: 0.17 (0.23), residues: 452 sheet: -1.67 (0.26), residues: 330 loop : -0.50 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 721 TYR 0.018 0.002 TYR A 306 PHE 0.018 0.002 PHE B 591 TRP 0.006 0.001 TRP A 623 HIS 0.003 0.001 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.28 (13926) covalent geometry : angle 0.69197 / 0.38 (19072) hydrogen bonds : bond 0.04316 / 2.66 ( 492) hydrogen bonds : angle 5.57347 / 3.86 ( 1336) *********************** 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 119 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8457 (p90) cc_final: 0.8087 (p90) REVERT: A 132 GLU cc_start: 0.7916 (pm20) cc_final: 0.7586 (pm20) REVERT: A 142 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 217 GLU cc_start: 0.8954 (tp30) cc_final: 0.8472 (mp0) REVERT: A 415 TYR cc_start: 0.8828 (m-80) cc_final: 0.8597 (m-10) REVERT: B 24 MET cc_start: 0.8202 (pmm) cc_final: 0.7909 (ptp) REVERT: B 81 PHE cc_start: 0.8333 (p90) cc_final: 0.8053 (p90) REVERT: B 132 GLU cc_start: 0.7891 (pm20) cc_final: 0.7552 (pm20) REVERT: B 142 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 217 GLU cc_start: 0.8943 (tp30) cc_final: 0.8423 (mp0) outliers start: 40 outliers final: 16 residues processed: 113 average time/residue: 0.3341 time to fit residues: 43.6452 Evaluate side-chains 90 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET 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 709 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.071284 restraints weight = 34596.808| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.42 r_work: 0.3131 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2614 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= 0.158 Angle : 0.613 7.499 19072 Z= 0.339 Chirality : 0.046 0.238 2088 Planarity : 0.003 0.025 2180 Dihedral : 17.283 155.192 2402 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.87 % Allowed : 11.60 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.21), residues: 1486 helix: 0.40 (0.24), residues: 452 sheet: -1.53 (0.27), residues: 324 loop : -0.38 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.017 0.001 TYR B 510 PHE 0.012 0.001 PHE A 61 TRP 0.007 0.001 TRP B 482 HIS 0.006 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (13926) covalent geometry : angle 0.61298 / 0.34 (19072) hydrogen bonds : bond 0.03815 / 2.35 ( 492) hydrogen bonds : angle 5.29788 / 3.66 ( 1336) *********************** 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 118 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8069 (pmm) cc_final: 0.7577 (ptp) REVERT: A 81 PHE cc_start: 0.8491 (p90) cc_final: 0.8140 (p90) REVERT: A 132 GLU cc_start: 0.7962 (pm20) cc_final: 0.7647 (pm20) REVERT: A 142 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8072 (tm-30) REVERT: A 217 GLU cc_start: 0.8913 (tp30) cc_final: 0.8469 (mp0) REVERT: A 259 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 415 TYR cc_start: 0.8822 (m-80) cc_final: 0.8588 (m-10) REVERT: B 81 PHE cc_start: 0.8512 (p90) cc_final: 0.8160 (p90) REVERT: B 132 GLU cc_start: 0.7980 (pm20) cc_final: 0.7664 (pm20) REVERT: B 142 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8129 (tm-30) REVERT: B 217 GLU cc_start: 0.8890 (tp30) cc_final: 0.8442 (mp0) outliers start: 25 outliers final: 14 residues processed: 114 average time/residue: 0.3517 time to fit residues: 45.9317 Evaluate side-chains 90 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 368 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 = 0.3656 r_free = 0.3656 target = 0.089474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.068120 restraints weight = 34818.031| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.36 r_work: 0.3060 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13926 Z= 0.293 Angle : 0.695 9.828 19072 Z= 0.376 Chirality : 0.048 0.255 2088 Planarity : 0.003 0.025 2180 Dihedral : 17.144 154.209 2398 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.32 % Allowed : 12.43 % Favored : 85.25 % 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: -0.74 (0.22), residues: 1486 helix: 0.38 (0.24), residues: 452 sheet: -1.54 (0.27), residues: 320 loop : -0.39 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 721 TYR 0.016 0.002 TYR A 306 PHE 0.018 0.002 PHE B 591 TRP 0.006 0.002 TRP B 482 HIS 0.003 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.29 (13926) covalent geometry : angle 0.69495 / 0.38 (19072) hydrogen bonds : bond 0.04264 / 2.65 ( 492) hydrogen bonds : angle 5.37562 / 3.72 ( 1336) *********************** 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 111 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8660 (p90) cc_final: 0.8324 (p90) REVERT: A 132 GLU cc_start: 0.8026 (pm20) cc_final: 0.7704 (pm20) REVERT: A 142 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 217 GLU cc_start: 0.8906 (tp30) cc_final: 0.8433 (mp0) REVERT: A 353 MET cc_start: 0.8196 (mmt) cc_final: 0.7825 (mmm) REVERT: A 365 ILE cc_start: 0.8836 (tp) cc_final: 0.8574 (tp) REVERT: A 415 TYR cc_start: 0.8845 (m-80) cc_final: 0.8583 (m-10) REVERT: B 24 MET cc_start: 0.8259 (pmm) cc_final: 0.7945 (ptp) REVERT: B 81 PHE cc_start: 0.8664 (p90) cc_final: 0.8334 (p90) REVERT: B 132 GLU cc_start: 0.8044 (pm20) cc_final: 0.7724 (pm20) REVERT: B 142 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8123 (tm-30) REVERT: B 217 GLU cc_start: 0.8934 (tp30) cc_final: 0.8444 (mp0) REVERT: B 353 MET cc_start: 0.8181 (mmt) cc_final: 0.7757 (mmm) REVERT: B 365 ILE cc_start: 0.8831 (tp) cc_final: 0.8566 (tp) REVERT: B 744 VAL cc_start: 0.9008 (t) cc_final: 0.8806 (p) outliers start: 31 outliers final: 16 residues processed: 103 average time/residue: 0.3956 time to fit residues: 46.1669 Evaluate side-chains 87 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.2980 chunk 138 optimal weight: 0.2980 chunk 83 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 274 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN B 274 HIS ** B 368 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 = 0.3703 r_free = 0.3703 target = 0.092167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071062 restraints weight = 34346.498| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.36 r_work: 0.3123 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13926 Z= 0.138 Angle : 0.619 8.349 19072 Z= 0.340 Chirality : 0.046 0.247 2088 Planarity : 0.003 0.029 2180 Dihedral : 17.074 156.728 2398 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.10 % Allowed : 12.65 % Favored : 85.25 % 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: 0.69 (0.24), residues: 450 sheet: -1.46 (0.27), residues: 328 loop : -0.17 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 743 TYR 0.017 0.001 TYR B 510 PHE 0.013 0.001 PHE A 425 TRP 0.010 0.001 TRP B 482 HIS 0.002 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (13926) covalent geometry : angle 0.61905 / 0.34 (19072) hydrogen bonds : bond 0.03645 / 2.24 ( 492) hydrogen bonds : angle 5.11761 / 3.53 ( 1336) *********************** 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 123 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8025 (pmm) cc_final: 0.7474 (ptp) REVERT: A 81 PHE cc_start: 0.8640 (p90) cc_final: 0.8324 (p90) REVERT: A 132 GLU cc_start: 0.7980 (pm20) cc_final: 0.7665 (pm20) REVERT: A 142 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8048 (tm-30) REVERT: A 191 MET cc_start: 0.7936 (mmt) cc_final: 0.7721 (mmp) REVERT: A 217 GLU cc_start: 0.8903 (tp30) cc_final: 0.8436 (mp0) REVERT: A 259 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 415 TYR cc_start: 0.8768 (m-80) cc_final: 0.8475 (m-10) REVERT: A 557 CYS cc_start: 0.9259 (m) cc_final: 0.9037 (p) REVERT: A 624 TYR cc_start: 0.8328 (m-80) cc_final: 0.8063 (m-10) REVERT: B 81 PHE cc_start: 0.8648 (p90) cc_final: 0.8349 (p90) REVERT: B 132 GLU cc_start: 0.8013 (pm20) cc_final: 0.7693 (pm20) REVERT: B 142 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8022 (tm-30) REVERT: B 191 MET cc_start: 0.7879 (mmt) cc_final: 0.7516 (mmp) REVERT: B 217 GLU cc_start: 0.8918 (tp30) cc_final: 0.8457 (mp0) REVERT: B 259 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8340 (mp) outliers start: 28 outliers final: 16 residues processed: 116 average time/residue: 0.4255 time to fit residues: 55.1846 Evaluate side-chains 93 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 274 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 274 HIS ** B 368 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 = 0.3677 r_free = 0.3677 target = 0.090000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068684 restraints weight = 34606.503| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.35 r_work: 0.3053 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13926 Z= 0.289 Angle : 0.721 12.793 19072 Z= 0.383 Chirality : 0.048 0.255 2088 Planarity : 0.003 0.027 2180 Dihedral : 17.037 155.280 2398 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.47 % Allowed : 12.72 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1486 helix: 0.66 (0.24), residues: 448 sheet: -1.46 (0.28), residues: 320 loop : -0.37 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 721 TYR 0.015 0.002 TYR B 510 PHE 0.020 0.002 PHE A 591 TRP 0.007 0.002 TRP A 482 HIS 0.005 0.001 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.29 (13926) covalent geometry : angle 0.72103 / 0.38 (19072) hydrogen bonds : bond 0.04132 / 2.56 ( 492) hydrogen bonds : angle 5.22660 / 3.62 ( 1336) *********************** 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 110 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8151 (pmm) cc_final: 0.7798 (ptp) REVERT: A 81 PHE cc_start: 0.8713 (p90) cc_final: 0.8409 (p90) REVERT: A 132 GLU cc_start: 0.8020 (pm20) cc_final: 0.7680 (pm20) REVERT: A 142 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8095 (tm-30) REVERT: A 217 GLU cc_start: 0.8896 (tp30) cc_final: 0.8408 (mp0) REVERT: A 365 ILE cc_start: 0.8833 (tp) cc_final: 0.8591 (tp) REVERT: A 415 TYR cc_start: 0.8790 (m-80) cc_final: 0.8486 (m-10) REVERT: B 24 MET cc_start: 0.8213 (pmm) cc_final: 0.7667 (ptp) REVERT: B 81 PHE cc_start: 0.8740 (p90) cc_final: 0.8442 (p90) REVERT: B 132 GLU cc_start: 0.8040 (pm20) cc_final: 0.7702 (pm20) REVERT: B 142 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8102 (tm-30) REVERT: B 217 GLU cc_start: 0.8915 (tp30) cc_final: 0.8418 (mp0) REVERT: B 365 ILE cc_start: 0.8838 (tp) cc_final: 0.8605 (tp) REVERT: B 744 VAL cc_start: 0.9019 (t) cc_final: 0.8745 (p) outliers start: 33 outliers final: 19 residues processed: 101 average time/residue: 0.3841 time to fit residues: 43.8922 Evaluate side-chains 93 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 368 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 = 0.3707 r_free = 0.3707 target = 0.091816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070695 restraints weight = 34454.433| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.35 r_work: 0.3113 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13926 Z= 0.151 Angle : 0.646 10.572 19072 Z= 0.348 Chirality : 0.045 0.259 2088 Planarity : 0.003 0.034 2180 Dihedral : 16.977 157.369 2398 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.87 % Allowed : 13.32 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1486 helix: 0.82 (0.24), residues: 448 sheet: -1.38 (0.27), residues: 332 loop : -0.24 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 743 TYR 0.016 0.001 TYR B 510 PHE 0.012 0.001 PHE B 749 TRP 0.008 0.001 TRP B 482 HIS 0.005 0.001 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (13926) covalent geometry : angle 0.64606 / 0.35 (19072) hydrogen bonds : bond 0.03659 / 2.23 ( 492) hydrogen bonds : angle 5.04565 / 3.48 ( 1336) *********************** 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 117 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.8124 (pmm) cc_final: 0.7746 (ptp) REVERT: A 81 PHE cc_start: 0.8701 (p90) cc_final: 0.8410 (p90) REVERT: A 132 GLU cc_start: 0.8034 (pm20) cc_final: 0.7694 (pm20) REVERT: A 142 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 217 GLU cc_start: 0.8880 (tp30) cc_final: 0.8417 (mp0) REVERT: A 365 ILE cc_start: 0.8775 (tp) cc_final: 0.8573 (tp) REVERT: A 415 TYR cc_start: 0.8687 (m-80) cc_final: 0.8388 (m-10) REVERT: A 557 CYS cc_start: 0.9268 (m) cc_final: 0.9061 (p) REVERT: B 24 MET cc_start: 0.8165 (pmm) cc_final: 0.7618 (ptp) REVERT: B 81 PHE cc_start: 0.8702 (p90) cc_final: 0.8422 (p90) REVERT: B 132 GLU cc_start: 0.8047 (pm20) cc_final: 0.7705 (pm20) REVERT: B 142 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7986 (tm-30) REVERT: B 191 MET cc_start: 0.7728 (mmt) cc_final: 0.7328 (mmp) REVERT: B 217 GLU cc_start: 0.8896 (tp30) cc_final: 0.8430 (mp0) REVERT: B 363 MET cc_start: 0.8648 (mmm) cc_final: 0.8444 (mmp) REVERT: B 365 ILE cc_start: 0.8769 (tp) cc_final: 0.8564 (tp) REVERT: B 557 CYS cc_start: 0.9247 (m) cc_final: 0.9041 (p) outliers start: 25 outliers final: 18 residues processed: 109 average time/residue: 0.3706 time to fit residues: 45.7465 Evaluate side-chains 98 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 304 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 149 optimal weight: 0.0040 chunk 140 optimal weight: 4.9990 chunk 99 optimal weight: 0.0770 chunk 142 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** B 368 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 = 0.3710 r_free = 0.3710 target = 0.091633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.070385 restraints weight = 34452.030| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.37 r_work: 0.3106 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13926 Z= 0.178 Angle : 0.673 12.132 19072 Z= 0.359 Chirality : 0.046 0.338 2088 Planarity : 0.003 0.066 2180 Dihedral : 16.935 156.990 2398 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.42 % Allowed : 14.00 % Favored : 84.58 % 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: -0.36 (0.22), residues: 1486 helix: 0.84 (0.24), residues: 450 sheet: -1.36 (0.28), residues: 332 loop : -0.23 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 743 TYR 0.016 0.001 TYR A 284 PHE 0.018 0.001 PHE B 61 TRP 0.002 0.001 TRP A 528 HIS 0.006 0.001 HIS B 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (13926) covalent geometry : angle 0.67267 / 0.36 (19072) hydrogen bonds : bond 0.03672 / 2.25 ( 492) hydrogen bonds : angle 5.02485 / 3.46 ( 1336) ********************** 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 102 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8140 (pmm) cc_final: 0.7784 (ptp) REVERT: A 81 PHE cc_start: 0.8765 (p90) cc_final: 0.8490 (p90) REVERT: A 132 GLU cc_start: 0.8032 (pm20) cc_final: 0.7690 (pm20) REVERT: A 142 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 191 MET cc_start: 0.7672 (mmp) cc_final: 0.7257 (mmp) REVERT: A 365 ILE cc_start: 0.8804 (tp) cc_final: 0.8598 (tp) REVERT: A 415 TYR cc_start: 0.8691 (m-80) cc_final: 0.8387 (m-10) REVERT: A 491 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8054 (mtm) REVERT: A 531 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8352 (mmmt) REVERT: A 557 CYS cc_start: 0.9286 (m) cc_final: 0.9074 (p) REVERT: B 24 MET cc_start: 0.8187 (pmm) cc_final: 0.7637 (ptp) REVERT: B 81 PHE cc_start: 0.8750 (p90) cc_final: 0.8485 (p90) REVERT: B 132 GLU cc_start: 0.8054 (pm20) cc_final: 0.7712 (pm20) REVERT: B 142 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7989 (tm-30) REVERT: B 191 MET cc_start: 0.7684 (mmt) cc_final: 0.7298 (mmp) REVERT: B 557 CYS cc_start: 0.9273 (m) cc_final: 0.9044 (p) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.4329 time to fit residues: 47.2915 Evaluate side-chains 95 residues out of total 1336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 539 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 709 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.2980 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.093302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072268 restraints weight = 34500.870| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.39 r_work: 0.3151 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13926 Z= 0.135 Angle : 0.651 11.908 19072 Z= 0.349 Chirality : 0.046 0.263 2088 Planarity : 0.003 0.049 2180 Dihedral : 16.845 157.929 2398 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.50 % Allowed : 14.45 % Favored : 84.06 % 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: -0.20 (0.22), residues: 1486 helix: 0.99 (0.24), residues: 448 sheet: -1.27 (0.28), residues: 332 loop : -0.15 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 743 TYR 0.014 0.001 TYR B 624 PHE 0.012 0.001 PHE B 61 TRP 0.008 0.001 TRP B 528 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (13926) covalent geometry : angle 0.65083 / 0.35 (19072) hydrogen bonds : bond 0.03467 / 2.13 ( 492) hydrogen bonds : angle 4.92370 / 3.38 ( 1336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2934.87 seconds wall clock time: 51 minutes 12.23 seconds (3072.23 seconds total)