Starting phenix.real_space_refine on Sat Jun 6 02:06:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11iy_75730/06_2026/11iy_75730.cif Found real_map, /net/cci-nas-00/data/ceres_data/11iy_75730/06_2026/11iy_75730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11iy_75730/06_2026/11iy_75730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11iy_75730/06_2026/11iy_75730.map" model { file = "/net/cci-nas-00/data/ceres_data/11iy_75730/06_2026/11iy_75730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11iy_75730/06_2026/11iy_75730.cif" } resolution = 3.57 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= 0.025 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7792 2.51 5 N 2072 2.21 5 O 2474 1.98 5 H 12082 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24452 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 12226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12226 Classifications: {'peptide': 790} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 56, 'TRANS': 731} Chain: "D" Number of atoms: 12226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 790, 12226 Classifications: {'peptide': 790} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 56, 'TRANS': 731} Time building chain proxies: 4.52, per 1000 atoms: 0.18 Number of scatterers: 24452 At special positions: 0 Unit cell: (92.4, 99.6, 330, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2474 8.00 N 2072 7.00 C 7792 6.00 H 12082 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 273 " - pdb=" SG CYS C 282 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 125 " distance=2.04 Simple disulfide: pdb=" SG CYS D 273 " - pdb=" SG CYS D 282 " distance=2.03 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: 2.71 Conformation dependent library (CDL) restraints added in 766.0 milliseconds 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 8.0% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.859A pdb=" N ASP C 87 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.900A pdb=" N ASP C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 338 through 341 Processing helix chain 'C' and resid 543 through 548 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 751 through 756 Processing helix chain 'C' and resid 764 through 766 No H-bonds generated for 'chain 'C' and resid 764 through 766' Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 84 through 88 removed outlier: 4.093A pdb=" N ASP D 87 " --> pdb=" O ASP D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.909A pdb=" N ASP D 207 " --> pdb=" O PRO D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 543 through 548 Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 751 through 756 Processing helix chain 'D' and resid 764 through 766 No H-bonds generated for 'chain 'D' and resid 764 through 766' Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 52 removed outlier: 5.902A pdb=" N THR C 47 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL C 141 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 49 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG C 143 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE C 51 " --> pdb=" O ARG C 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 93 Processing sheet with id=AA3, first strand: chain 'C' and resid 151 through 152 Processing sheet with id=AA4, first strand: chain 'C' and resid 156 through 162 removed outlier: 5.769A pdb=" N TYR C 157 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP C 259 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA C 159 " --> pdb=" O ASP C 259 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU C 261 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL C 161 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 236 " --> pdb=" O GLN C 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 170 through 172 removed outlier: 6.658A pdb=" N VAL C 219 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 268 through 270 Processing sheet with id=AA7, first strand: chain 'C' and resid 286 through 292 Processing sheet with id=AA8, first strand: chain 'C' and resid 343 through 345 Processing sheet with id=AA9, first strand: chain 'C' and resid 405 through 407 removed outlier: 3.811A pdb=" N HIS C 447 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AB2, first strand: chain 'C' and resid 457 through 459 Processing sheet with id=AB3, first strand: chain 'C' and resid 518 through 524 removed outlier: 6.711A pdb=" N TYR C 519 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N GLU C 609 " --> pdb=" O TYR C 519 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL C 521 " --> pdb=" O GLU C 609 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LEU C 611 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL C 523 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS C 604 " --> pdb=" O VAL C 588 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR C 587 " --> pdb=" O LEU C 554 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.849A pdb=" N VAL C 570 " --> pdb=" O VAL C 533 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 625 through 631 removed outlier: 5.855A pdb=" N TYR C 626 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL C 711 " --> pdb=" O TYR C 626 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU C 628 " --> pdb=" O VAL C 711 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR C 713 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 630 " --> pdb=" O THR C 713 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR C 654 " --> pdb=" O SER C 696 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 639 through 642 removed outlier: 6.295A pdb=" N LEU C 675 " --> pdb=" O LEU C 640 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 721 through 722 Processing sheet with id=AB8, first strand: chain 'C' and resid 729 through 733 removed outlier: 6.454A pdb=" N LEU C 730 " --> pdb=" O LYS C 813 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU C 815 " --> pdb=" O LEU C 730 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 732 " --> pdb=" O LEU C 815 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 768 through 770 Processing sheet with id=AC1, first strand: chain 'D' and resid 46 through 52 removed outlier: 5.912A pdb=" N THR D 47 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL D 141 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL D 49 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ARG D 143 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 51 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 90 through 93 Processing sheet with id=AC3, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AC4, first strand: chain 'D' and resid 156 through 162 removed outlier: 5.706A pdb=" N TYR D 157 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP D 259 " --> pdb=" O TYR D 157 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA D 159 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU D 261 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 161 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D 236 " --> pdb=" O GLN D 197 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 170 through 172 removed outlier: 6.670A pdb=" N VAL D 219 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 268 through 270 Processing sheet with id=AC7, first strand: chain 'D' and resid 286 through 292 Processing sheet with id=AC8, first strand: chain 'D' and resid 343 through 345 Processing sheet with id=AC9, first strand: chain 'D' and resid 405 through 407 removed outlier: 3.861A pdb=" N HIS D 447 " --> pdb=" O PHE D 489 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 431 through 432 Processing sheet with id=AD2, first strand: chain 'D' and resid 457 through 459 Processing sheet with id=AD3, first strand: chain 'D' and resid 518 through 524 removed outlier: 6.741A pdb=" N TYR D 519 " --> pdb=" O TYR D 607 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N GLU D 609 " --> pdb=" O TYR D 519 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL D 521 " --> pdb=" O GLU D 609 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU D 611 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL D 523 " --> pdb=" O LEU D 611 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 604 " --> pdb=" O VAL D 588 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 588 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 587 " --> pdb=" O LEU D 554 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 532 through 533 removed outlier: 3.783A pdb=" N VAL D 570 " --> pdb=" O VAL D 533 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 625 through 631 removed outlier: 6.011A pdb=" N TYR D 626 " --> pdb=" O ASN D 709 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL D 711 " --> pdb=" O TYR D 626 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU D 628 " --> pdb=" O VAL D 711 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N THR D 713 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL D 630 " --> pdb=" O THR D 713 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR D 654 " --> pdb=" O SER D 696 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 639 through 642 removed outlier: 6.069A pdb=" N LEU D 675 " --> pdb=" O LEU D 640 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 721 through 722 Processing sheet with id=AD8, first strand: chain 'D' and resid 729 through 733 removed outlier: 6.439A pdb=" N LEU D 730 " --> pdb=" O LYS D 813 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU D 815 " --> pdb=" O LEU D 730 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL D 732 " --> pdb=" O LEU D 815 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 768 through 770 275 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12080 1.03 - 1.23: 22 1.23 - 1.43: 5162 1.43 - 1.62: 7400 1.62 - 1.82: 54 Bond restraints: 24718 Sorted by residual: bond pdb=" C HIS D 802 " pdb=" O HIS D 802 " ideal model delta sigma weight residual 1.235 1.226 0.009 4.70e-03 4.53e+04 3.88e+00 bond pdb=" CA HIS D 378 " pdb=" C HIS D 378 " ideal model delta sigma weight residual 1.531 1.521 0.010 7.40e-03 1.83e+04 1.82e+00 bond pdb=" CA LEU C 380 " pdb=" C LEU C 380 " ideal model delta sigma weight residual 1.534 1.521 0.013 9.50e-03 1.11e+04 1.80e+00 bond pdb=" CA HIS C 378 " pdb=" CB HIS C 378 " ideal model delta sigma weight residual 1.522 1.532 -0.009 7.00e-03 2.04e+04 1.80e+00 bond pdb=" CA LEU D 380 " pdb=" C LEU D 380 " ideal model delta sigma weight residual 1.534 1.521 0.013 9.50e-03 1.11e+04 1.76e+00 ... (remaining 24713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 42986 1.39 - 2.79: 1574 2.79 - 4.18: 188 4.18 - 5.58: 20 5.58 - 6.97: 4 Bond angle restraints: 44772 Sorted by residual: angle pdb=" C GLY C 377 " pdb=" N HIS C 378 " pdb=" CA HIS C 378 " ideal model delta sigma weight residual 122.83 119.09 3.74 1.08e+00 8.57e-01 1.20e+01 angle pdb=" C PHE D 400 " pdb=" N THR D 401 " pdb=" CA THR D 401 " ideal model delta sigma weight residual 121.33 126.14 -4.81 1.40e+00 5.10e-01 1.18e+01 angle pdb=" C PHE C 400 " pdb=" N THR C 401 " pdb=" CA THR C 401 " ideal model delta sigma weight residual 121.33 125.97 -4.64 1.40e+00 5.10e-01 1.10e+01 angle pdb=" N ALA C 786 " pdb=" CA ALA C 786 " pdb=" CB ALA C 786 " ideal model delta sigma weight residual 114.17 110.43 3.74 1.14e+00 7.69e-01 1.08e+01 angle pdb=" N GLU D 439 " pdb=" CA GLU D 439 " pdb=" C GLU D 439 " ideal model delta sigma weight residual 108.55 113.18 -4.63 1.62e+00 3.81e-01 8.17e+00 ... (remaining 44767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10596 17.96 - 35.91: 756 35.91 - 53.87: 226 53.87 - 71.83: 197 71.83 - 89.79: 11 Dihedral angle restraints: 11786 sinusoidal: 6544 harmonic: 5242 Sorted by residual: dihedral pdb=" CA LEU D 271 " pdb=" C LEU D 271 " pdb=" N PRO D 272 " pdb=" CA PRO D 272 " ideal model delta harmonic sigma weight residual 180.00 137.64 42.36 0 5.00e+00 4.00e-02 7.18e+01 dihedral pdb=" CA LEU C 271 " pdb=" C LEU C 271 " pdb=" N PRO C 272 " pdb=" CA PRO C 272 " ideal model delta harmonic sigma weight residual 180.00 137.69 42.31 0 5.00e+00 4.00e-02 7.16e+01 dihedral pdb=" CA TYR D 399 " pdb=" C TYR D 399 " pdb=" N PHE D 400 " pdb=" CA PHE D 400 " ideal model delta harmonic sigma weight residual -180.00 -137.92 -42.08 0 5.00e+00 4.00e-02 7.08e+01 ... (remaining 11783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1325 0.037 - 0.074: 405 0.074 - 0.111: 215 0.111 - 0.149: 68 0.149 - 0.186: 5 Chirality restraints: 2018 Sorted by residual: chirality pdb=" CA ILE D 608 " pdb=" N ILE D 608 " pdb=" C ILE D 608 " pdb=" CB ILE D 608 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA ILE D 572 " pdb=" N ILE D 572 " pdb=" C ILE D 572 " pdb=" CB ILE D 572 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE C 572 " pdb=" N ILE C 572 " pdb=" C ILE C 572 " pdb=" CB ILE C 572 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 2015 not shown) Planarity restraints: 3768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 390 " 0.030 2.00e-02 2.50e+03 5.77e-02 3.33e+01 pdb=" N LEU D 391 " -0.099 2.00e-02 2.50e+03 pdb=" CA LEU D 391 " 0.026 2.00e-02 2.50e+03 pdb=" H LEU D 391 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 188 " 0.027 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" N ASN C 189 " -0.089 2.00e-02 2.50e+03 pdb=" CA ASN C 189 " 0.023 2.00e-02 2.50e+03 pdb=" H ASN C 189 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 368 " -0.027 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" N VAL D 369 " 0.088 2.00e-02 2.50e+03 pdb=" CA VAL D 369 " -0.022 2.00e-02 2.50e+03 pdb=" H VAL D 369 " -0.039 2.00e-02 2.50e+03 ... (remaining 3765 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 860 2.14 - 2.75: 46022 2.75 - 3.37: 67727 3.37 - 3.98: 86150 3.98 - 4.60: 130946 Nonbonded interactions: 331705 Sorted by model distance: nonbonded pdb=" OE1 GLN D 472 " pdb=" H VAL D 474 " model vdw 1.521 2.450 nonbonded pdb=" OE1 GLN C 472 " pdb=" H VAL C 474 " model vdw 1.535 2.450 nonbonded pdb=" OD2 ASP D 144 " pdb=" H ASP D 186 " model vdw 1.537 2.450 nonbonded pdb=" H SER C 528 " pdb=" OD2 ASP C 531 " model vdw 1.574 2.450 nonbonded pdb="HH21 ARG C 360 " pdb=" O LEU C 391 " model vdw 1.576 2.450 ... (remaining 331700 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.580 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12640 Z= 0.149 Angle : 0.705 6.969 17310 Z= 0.392 Chirality : 0.048 0.186 2018 Planarity : 0.007 0.141 2306 Dihedral : 13.921 89.786 4688 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.19 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.34 % 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: -1.56 (0.20), residues: 1576 helix: -3.23 (0.49), residues: 36 sheet: 0.01 (0.21), residues: 508 loop : -1.59 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 232 TYR 0.043 0.005 TYR C 233 PHE 0.017 0.002 PHE D 366 TRP 0.009 0.002 TRP C 32 HIS 0.008 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (12636) covalent geometry : angle 0.70276 / 0.39 (17302) SS BOND : bond 0.00482 / 0.24 ( 4) SS BOND : angle 2.53515 / 1.63 ( 8) hydrogen bonds : bond 0.24293 / 15.56 ( 275) hydrogen bonds : angle 9.98567 / 6.69 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.577 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 549 ILE cc_start: 0.5850 (mt) cc_final: 0.5645 (mt) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2642 time to fit residues: 92.0608 Evaluate side-chains 125 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN C 396 GLN D 146 ASN D 189 ASN D 394 ASN D 396 GLN D 614 ASN D 623 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.216771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154016 restraints weight = 60579.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.157317 restraints weight = 34489.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.157197 restraints weight = 24396.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.157229 restraints weight = 20615.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.157412 restraints weight = 19835.728| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12640 Z= 0.183 Angle : 0.719 8.591 17310 Z= 0.379 Chirality : 0.050 0.181 2018 Planarity : 0.006 0.064 2306 Dihedral : 7.546 44.860 1728 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.69 % Favored : 90.61 % Rotamer: Outliers : 1.14 % Allowed : 7.56 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.27 % 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: -1.53 (0.20), residues: 1576 helix: -3.00 (0.76), residues: 24 sheet: 0.26 (0.21), residues: 504 loop : -1.74 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 250 TYR 0.024 0.002 TYR C 399 PHE 0.026 0.002 PHE D 449 TRP 0.007 0.001 TRP D 89 HIS 0.007 0.001 HIS D 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (12636) covalent geometry : angle 0.71858 / 0.38 (17302) SS BOND : bond 0.00238 / 0.12 ( 4) SS BOND : angle 1.37476 / 0.89 ( 8) hydrogen bonds : bond 0.05261 / 3.43 ( 275) hydrogen bonds : angle 7.98527 / 5.27 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.595 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 THR cc_start: 0.7838 (m) cc_final: 0.7614 (p) REVERT: C 362 PHE cc_start: 0.6918 (m-80) cc_final: 0.6685 (m-80) REVERT: D 644 GLN cc_start: 0.8417 (tp40) cc_final: 0.7819 (tm-30) outliers start: 16 outliers final: 13 residues processed: 152 average time/residue: 0.2319 time to fit residues: 51.6303 Evaluate side-chains 126 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 513 THR Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 654 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 136 optimal weight: 1.9990 chunk 154 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 87 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN D 247 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.214296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.149440 restraints weight = 60640.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151268 restraints weight = 35190.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.151616 restraints weight = 25434.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.152185 restraints weight = 20353.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152416 restraints weight = 19537.631| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12640 Z= 0.175 Angle : 0.674 8.285 17310 Z= 0.352 Chirality : 0.048 0.154 2018 Planarity : 0.005 0.064 2306 Dihedral : 7.057 41.170 1728 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.20 % Favored : 90.16 % Rotamer: Outliers : 1.78 % Allowed : 8.13 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 2.59 % Twisted General : 0.27 % 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: -1.57 (0.20), residues: 1576 helix: -3.16 (0.71), residues: 24 sheet: 0.00 (0.21), residues: 492 loop : -1.60 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 250 TYR 0.016 0.001 TYR D 584 PHE 0.020 0.002 PHE D 449 TRP 0.008 0.002 TRP D 89 HIS 0.004 0.001 HIS C 363 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (12636) covalent geometry : angle 0.67400 / 0.35 (17302) SS BOND : bond 0.00267 / 0.13 ( 4) SS BOND : angle 1.35839 / 0.88 ( 8) hydrogen bonds : bond 0.04684 / 3.12 ( 275) hydrogen bonds : angle 7.18955 / 4.74 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.659 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 130 average time/residue: 0.2308 time to fit residues: 43.9792 Evaluate side-chains 123 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 422 SER Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.213199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150181 restraints weight = 59783.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.152281 restraints weight = 33920.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150683 restraints weight = 22105.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.151175 restraints weight = 24512.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.151276 restraints weight = 21797.860| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12640 Z= 0.152 Angle : 0.641 7.314 17310 Z= 0.330 Chirality : 0.048 0.157 2018 Planarity : 0.005 0.062 2306 Dihedral : 6.678 40.400 1728 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.63 % Allowed : 8.95 % Favored : 90.42 % Rotamer: Outliers : 1.50 % Allowed : 8.92 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.27 % 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: -1.57 (0.20), residues: 1576 helix: -3.09 (0.70), residues: 24 sheet: -0.06 (0.22), residues: 492 loop : -1.58 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 360 TYR 0.018 0.001 TYR D 399 PHE 0.022 0.001 PHE D 449 TRP 0.007 0.001 TRP C 89 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (12636) covalent geometry : angle 0.64112 / 0.33 (17302) SS BOND : bond 0.00230 / 0.11 ( 4) SS BOND : angle 1.15504 / 0.74 ( 8) hydrogen bonds : bond 0.03703 / 2.44 ( 275) hydrogen bonds : angle 6.70206 / 4.40 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.637 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: symmetry clash revert: symmetry clash REVERT: D 65 MET cc_start: 0.3427 (mmm) cc_final: 0.2925 (tpt) outliers start: 21 outliers final: 16 residues processed: 114 average time/residue: 0.2284 time to fit residues: 38.8669 Evaluate side-chains 111 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 69 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.214101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.172556 restraints weight = 62204.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.163901 restraints weight = 69731.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.158629 restraints weight = 45706.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.157713 restraints weight = 48468.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.159316 restraints weight = 37848.232| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12640 Z= 0.161 Angle : 0.630 6.855 17310 Z= 0.325 Chirality : 0.048 0.151 2018 Planarity : 0.005 0.064 2306 Dihedral : 6.529 40.385 1728 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.39 % Favored : 90.10 % Rotamer: Outliers : 1.85 % Allowed : 9.77 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.27 % 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: -1.64 (0.20), residues: 1576 helix: -2.89 (0.75), residues: 24 sheet: -0.23 (0.22), residues: 532 loop : -1.60 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 360 TYR 0.014 0.001 TYR C 584 PHE 0.019 0.001 PHE D 449 TRP 0.006 0.001 TRP C 89 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12636) covalent geometry : angle 0.62973 / 0.32 (17302) SS BOND : bond 0.00327 / 0.16 ( 4) SS BOND : angle 1.51135 / 0.96 ( 8) hydrogen bonds : bond 0.03625 / 2.39 ( 275) hydrogen bonds : angle 6.50441 / 4.28 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.555 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: symmetry clash REVERT: C 255 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.6468 (t) outliers start: 26 outliers final: 18 residues processed: 115 average time/residue: 0.2169 time to fit residues: 37.9573 Evaluate side-chains 107 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 134 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.212640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.170581 restraints weight = 62033.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.158661 restraints weight = 67613.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.152702 restraints weight = 57286.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.153119 restraints weight = 50211.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.154310 restraints weight = 40992.797| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12640 Z= 0.180 Angle : 0.641 7.501 17310 Z= 0.331 Chirality : 0.048 0.159 2018 Planarity : 0.005 0.067 2306 Dihedral : 6.504 41.231 1728 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.33 % Favored : 90.16 % Rotamer: Outliers : 2.50 % Allowed : 9.63 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.27 % 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: -1.65 (0.20), residues: 1576 helix: -3.14 (0.65), residues: 24 sheet: -0.31 (0.22), residues: 532 loop : -1.55 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 360 TYR 0.017 0.001 TYR D 399 PHE 0.019 0.001 PHE D 449 TRP 0.005 0.001 TRP C 89 HIS 0.004 0.001 HIS C 601 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (12636) covalent geometry : angle 0.64103 / 0.33 (17302) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 1.22690 / 0.79 ( 8) hydrogen bonds : bond 0.03588 / 2.34 ( 275) hydrogen bonds : angle 6.45082 / 4.24 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.666 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: symmetry clash REVERT: C 255 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.6497 (t) REVERT: D 498 VAL cc_start: 0.6829 (OUTLIER) cc_final: 0.6592 (t) outliers start: 35 outliers final: 26 residues processed: 119 average time/residue: 0.2103 time to fit residues: 38.2024 Evaluate side-chains 113 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 VAL Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 718 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.208045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.171521 restraints weight = 61623.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.164888 restraints weight = 70859.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.161988 restraints weight = 66458.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161820 restraints weight = 55414.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.161538 restraints weight = 37376.591| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 12640 Z= 0.322 Angle : 0.749 7.440 17310 Z= 0.395 Chirality : 0.051 0.214 2018 Planarity : 0.006 0.088 2306 Dihedral : 6.879 42.872 1728 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.51 % Allowed : 11.68 % Favored : 87.82 % Rotamer: Outliers : 2.92 % Allowed : 10.13 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 2.59 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.20), residues: 1576 helix: -3.01 (0.70), residues: 24 sheet: -0.53 (0.22), residues: 520 loop : -1.93 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 242 TYR 0.024 0.002 TYR C 584 PHE 0.026 0.002 PHE C 270 TRP 0.006 0.001 TRP C 89 HIS 0.009 0.002 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.32 (12636) covalent geometry : angle 0.74811 / 0.39 (17302) SS BOND : bond 0.00581 / 0.28 ( 4) SS BOND : angle 1.97155 / 1.25 ( 8) hydrogen bonds : bond 0.04192 / 2.78 ( 275) hydrogen bonds : angle 6.78382 / 4.48 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.556 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: symmetry clash REVERT: C 143 ARG cc_start: 0.6778 (mmp-170) cc_final: 0.6574 (mmm160) REVERT: C 208 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8726 (t) REVERT: C 255 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7919 (m) REVERT: D 208 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8450 (t) outliers start: 41 outliers final: 32 residues processed: 116 average time/residue: 0.2168 time to fit residues: 38.4111 Evaluate side-chains 110 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 359 ASN Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 106 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.211925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.172425 restraints weight = 62038.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.156567 restraints weight = 75230.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.152836 restraints weight = 77084.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.153587 restraints weight = 60209.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.154641 restraints weight = 43888.148| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12640 Z= 0.127 Angle : 0.623 7.821 17310 Z= 0.318 Chirality : 0.048 0.147 2018 Planarity : 0.005 0.063 2306 Dihedral : 6.509 40.946 1728 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.01 % Favored : 90.48 % Rotamer: Outliers : 1.78 % Allowed : 11.41 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.20), residues: 1576 helix: -3.01 (0.69), residues: 24 sheet: -0.33 (0.22), residues: 520 loop : -1.67 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 360 TYR 0.018 0.001 TYR D 399 PHE 0.018 0.001 PHE D 449 TRP 0.005 0.001 TRP C 89 HIS 0.003 0.001 HIS C 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (12636) covalent geometry : angle 0.62251 / 0.32 (17302) SS BOND : bond 0.00249 / 0.12 ( 4) SS BOND : angle 1.21006 / 0.77 ( 8) hydrogen bonds : bond 0.03370 / 2.19 ( 275) hydrogen bonds : angle 6.35768 / 4.20 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.584 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: C 255 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.6334 (t) REVERT: C 362 PHE cc_start: 0.6675 (m-80) cc_final: 0.6405 (m-80) outliers start: 25 outliers final: 22 residues processed: 103 average time/residue: 0.2324 time to fit residues: 35.3177 Evaluate side-chains 101 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.211560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.170404 restraints weight = 61796.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.156949 restraints weight = 72172.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150110 restraints weight = 58721.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.149926 restraints weight = 51286.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.150785 restraints weight = 44332.235| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12640 Z= 0.145 Angle : 0.627 8.851 17310 Z= 0.320 Chirality : 0.048 0.150 2018 Planarity : 0.005 0.063 2306 Dihedral : 6.413 41.450 1728 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.03 % Favored : 89.47 % Rotamer: Outliers : 1.93 % Allowed : 11.55 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1576 helix: -3.00 (0.70), residues: 24 sheet: -0.28 (0.22), residues: 520 loop : -1.59 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 360 TYR 0.014 0.001 TYR D 399 PHE 0.013 0.001 PHE D 449 TRP 0.005 0.001 TRP C 89 HIS 0.007 0.001 HIS D 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (12636) covalent geometry : angle 0.62683 / 0.32 (17302) SS BOND : bond 0.00258 / 0.13 ( 4) SS BOND : angle 1.10181 / 0.70 ( 8) hydrogen bonds : bond 0.03354 / 2.18 ( 275) hydrogen bonds : angle 6.22688 / 4.11 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.560 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: C 143 ARG cc_start: 0.7451 (mmp-170) cc_final: 0.6723 (mmm160) REVERT: C 255 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.6363 (t) outliers start: 27 outliers final: 26 residues processed: 102 average time/residue: 0.2509 time to fit residues: 37.5549 Evaluate side-chains 105 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 655 TYR Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 22 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 117 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.212153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.171256 restraints weight = 62345.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.155490 restraints weight = 72370.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150096 restraints weight = 58404.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.150541 restraints weight = 48371.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.151359 restraints weight = 38122.540| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12640 Z= 0.133 Angle : 0.609 9.620 17310 Z= 0.309 Chirality : 0.047 0.150 2018 Planarity : 0.005 0.060 2306 Dihedral : 6.249 40.122 1728 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.20 % Favored : 90.23 % Rotamer: Outliers : 1.78 % Allowed : 11.48 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.21), residues: 1576 helix: -2.96 (0.71), residues: 24 sheet: -0.34 (0.22), residues: 536 loop : -1.57 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 360 TYR 0.015 0.001 TYR D 399 PHE 0.022 0.001 PHE D 449 TRP 0.003 0.001 TRP C 89 HIS 0.012 0.001 HIS D 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (12636) covalent geometry : angle 0.60864 / 0.31 (17302) SS BOND : bond 0.00272 / 0.13 ( 4) SS BOND : angle 1.10701 / 0.70 ( 8) hydrogen bonds : bond 0.03233 / 2.10 ( 275) hydrogen bonds : angle 6.04905 / 3.99 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3152 Ramachandran restraints generated. 1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.752 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: C 143 ARG cc_start: 0.7430 (mmp-170) cc_final: 0.6644 (mmm160) REVERT: C 255 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.6300 (t) REVERT: C 487 THR cc_start: 0.6208 (OUTLIER) cc_final: 0.5863 (p) REVERT: D 699 ARG cc_start: 0.7253 (ptp-110) cc_final: 0.6997 (ptp-110) outliers start: 25 outliers final: 23 residues processed: 99 average time/residue: 0.2422 time to fit residues: 35.0999 Evaluate side-chains 101 residues out of total 1402 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 114 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 504 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 247 ASN Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 655 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 53 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 131 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.211663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.174106 restraints weight = 61997.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.162836 restraints weight = 71022.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.160842 restraints weight = 71303.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162551 restraints weight = 50271.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.163344 restraints weight = 40254.711| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12640 Z= 0.144 Angle : 0.616 9.507 17310 Z= 0.313 Chirality : 0.047 0.149 2018 Planarity : 0.005 0.061 2306 Dihedral : 6.218 40.824 1728 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.03 % Favored : 89.53 % Rotamer: Outliers : 2.07 % Allowed : 11.27 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.21), residues: 1576 helix: -2.93 (0.72), residues: 24 sheet: -0.23 (0.23), residues: 494 loop : -1.46 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 360 TYR 0.013 0.001 TYR C 482 PHE 0.016 0.001 PHE D 449 TRP 0.004 0.001 TRP C 89 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (12636) covalent geometry : angle 0.61564 / 0.31 (17302) SS BOND : bond 0.00284 / 0.14 ( 4) SS BOND : angle 1.11714 / 0.71 ( 8) hydrogen bonds : bond 0.03195 / 2.08 ( 275) hydrogen bonds : angle 5.99936 / 3.97 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4427.48 seconds wall clock time: 75 minutes 56.04 seconds (4556.04 seconds total)