Starting phenix.real_space_refine on Fri Sep 11 19:21:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.cif Found real_map, /net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6of2_20040/09_2026/6of2_20040.cif" } resolution = 2.9 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= 0.005 sd= 0.705 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 7048 2.51 5 N 1930 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11062 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 4048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4048 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 52, 'TRANS': 475} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: D, E Time building chain proxies: 4.41, per 1000 atoms: 0.40 Number of scatterers: 11062 At special positions: 0 Unit cell: (145.8, 87.48, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 6 15.00 Mg 2 11.99 O 2020 8.00 N 1930 7.00 C 7048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 40.1% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 4.074A pdb=" N LEU A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 93 through 115 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 134 through 147 removed outlier: 4.064A pdb=" N VAL A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 4.164A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 203 removed outlier: 3.637A pdb=" N LEU B 200 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 211 removed outlier: 3.561A pdb=" N ASN B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 242 through 257 removed outlier: 3.603A pdb=" N ASN B 246 " --> pdb=" O HIS B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 367 through 387 Processing helix chain 'B' and resid 403 through 417 Processing helix chain 'B' and resid 429 through 443 removed outlier: 3.642A pdb=" N SER B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 Processing helix chain 'B' and resid 535 through 544 removed outlier: 4.160A pdb=" N SER B 540 " --> pdb=" O PRO B 536 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.506A pdb=" N SER B 660 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 691 removed outlier: 4.340A pdb=" N TYR B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 4.074A pdb=" N LEU D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 41 through 64 Processing helix chain 'D' and resid 67 through 84 Processing helix chain 'D' and resid 93 through 115 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 134 through 147 removed outlier: 4.062A pdb=" N VAL D 138 " --> pdb=" O PRO D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 4.165A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 203 removed outlier: 3.636A pdb=" N LEU E 200 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 203 " --> pdb=" O GLY E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 211 removed outlier: 3.560A pdb=" N ASN E 207 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Proline residue: E 208 - end of helix Processing helix chain 'E' and resid 242 through 257 removed outlier: 3.603A pdb=" N ASN E 246 " --> pdb=" O HIS E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 330 through 334 Processing helix chain 'E' and resid 367 through 387 Processing helix chain 'E' and resid 403 through 417 Processing helix chain 'E' and resid 429 through 443 removed outlier: 3.642A pdb=" N SER E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 484 Processing helix chain 'E' and resid 535 through 544 removed outlier: 4.160A pdb=" N SER E 540 " --> pdb=" O PRO E 536 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP E 541 " --> pdb=" O GLU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 660 removed outlier: 3.507A pdb=" N SER E 660 " --> pdb=" O SER E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 676 through 691 removed outlier: 4.341A pdb=" N TYR E 680 " --> pdb=" O PRO E 676 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL E 681 " --> pdb=" O THR E 677 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY E 683 " --> pdb=" O ALA E 679 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU E 684 " --> pdb=" O TYR E 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349 removed outlier: 7.530A pdb=" N GLU B 646 " --> pdb=" O VAL B 638 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL B 638 " --> pdb=" O GLU B 646 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS B 648 " --> pdb=" O ARG B 636 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU B 550 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 632 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET B 548 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL B 188 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 190 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 143 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL B 188 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 190 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 351 through 358 removed outlier: 6.812A pdb=" N LEU B 320 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N MET B 356 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 318 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET B 301 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN B 396 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 303 " --> pdb=" O ASN B 396 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU B 264 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 263 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU B 422 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE B 265 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 349 removed outlier: 7.530A pdb=" N GLU E 646 " --> pdb=" O VAL E 638 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL E 638 " --> pdb=" O GLU E 646 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS E 648 " --> pdb=" O ARG E 636 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU E 550 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU E 632 " --> pdb=" O MET E 548 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET E 548 " --> pdb=" O LEU E 632 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL E 188 " --> pdb=" O HIS E 150 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU E 190 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY E 143 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 122 through 125 removed outlier: 6.503A pdb=" N VAL E 188 " --> pdb=" O HIS E 150 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU E 190 " --> pdb=" O LYS E 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 137 through 139 Processing sheet with id=AB3, first strand: chain 'E' and resid 351 through 358 removed outlier: 6.812A pdb=" N LEU E 320 " --> pdb=" O VAL E 354 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET E 356 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL E 318 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET E 301 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN E 396 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU E 303 " --> pdb=" O ASN E 396 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU E 264 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE E 263 " --> pdb=" O GLU E 420 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU E 422 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE E 265 " --> pdb=" O LEU E 422 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1470 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: 2.02 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 3823 1.37 - 1.51: 3947 1.51 - 1.66: 3502 1.66 - 1.80: 76 1.80 - 1.94: 14 Bond restraints: 11362 Sorted by residual: bond pdb=" O3G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" O3G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.558 1.504 0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" O2G AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.557 1.505 0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" O2G AGS B 801 " pdb=" PG AGS B 801 " ideal model delta sigma weight residual 1.557 1.505 0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" O3B AGS E 801 " pdb=" PG AGS E 801 " ideal model delta sigma weight residual 1.559 1.605 -0.046 2.00e-02 2.50e+03 5.20e+00 ... (remaining 11357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 14375 1.72 - 3.45: 928 3.45 - 5.17: 151 5.17 - 6.89: 36 6.89 - 8.62: 26 Bond angle restraints: 15516 Sorted by residual: angle pdb=" N PRO E 455 " pdb=" CA PRO E 455 " pdb=" CB PRO E 455 " ideal model delta sigma weight residual 103.00 110.62 -7.62 1.10e+00 8.26e-01 4.79e+01 angle pdb=" N PRO B 455 " pdb=" CA PRO B 455 " pdb=" CB PRO B 455 " ideal model delta sigma weight residual 103.00 110.58 -7.58 1.10e+00 8.26e-01 4.74e+01 angle pdb=" C TYR E 225 " pdb=" N THR E 226 " pdb=" CA THR E 226 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C TYR B 225 " pdb=" N THR B 226 " pdb=" CA THR B 226 " ideal model delta sigma weight residual 121.54 130.12 -8.58 1.91e+00 2.74e-01 2.02e+01 angle pdb=" N ASN E 185 " pdb=" CA ASN E 185 " pdb=" C ASN E 185 " ideal model delta sigma weight residual 110.42 116.89 -6.47 1.46e+00 4.69e-01 1.96e+01 ... (remaining 15511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.46: 6572 32.46 - 64.92: 182 64.92 - 97.38: 4 97.38 - 129.84: 0 129.84 - 162.30: 2 Dihedral angle restraints: 6760 sinusoidal: 2668 harmonic: 4092 Sorted by residual: dihedral pdb=" CA ARG B 295 " pdb=" C ARG B 295 " pdb=" N SER B 296 " pdb=" CA SER B 296 " ideal model delta harmonic sigma weight residual 180.00 -130.21 -49.79 0 5.00e+00 4.00e-02 9.92e+01 dihedral pdb=" CA ARG E 295 " pdb=" C ARG E 295 " pdb=" N SER E 296 " pdb=" CA SER E 296 " ideal model delta harmonic sigma weight residual -180.00 -130.24 -49.76 0 5.00e+00 4.00e-02 9.90e+01 dihedral pdb=" O1A AGS E 801 " pdb=" O3A AGS E 801 " pdb=" PA AGS E 801 " pdb=" PB AGS E 801 " ideal model delta sinusoidal sigma weight residual -67.73 94.57 -162.30 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 6757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1202 0.047 - 0.094: 402 0.094 - 0.141: 114 0.141 - 0.188: 16 0.188 - 0.235: 4 Chirality restraints: 1738 Sorted by residual: chirality pdb=" CA PRO B 455 " pdb=" N PRO B 455 " pdb=" C PRO B 455 " pdb=" CB PRO B 455 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PRO E 455 " pdb=" N PRO E 455 " pdb=" C PRO E 455 " pdb=" CB PRO E 455 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA PHE B 673 " pdb=" N PHE B 673 " pdb=" C PHE B 673 " pdb=" CB PHE B 673 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 1735 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 451 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO E 452 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 452 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 451 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 452 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 486 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO E 487 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 487 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 487 " 0.026 5.00e-02 4.00e+02 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 100 2.63 - 3.20: 10210 3.20 - 3.76: 15367 3.76 - 4.33: 20302 4.33 - 4.90: 35675 Nonbonded interactions: 81654 Sorted by model distance: nonbonded pdb=" O3G AGS B 801 " pdb="MG MG B 802 " model vdw 2.062 2.170 nonbonded pdb=" O3G AGS E 801 " pdb="MG MG E 802 " model vdw 2.063 2.170 nonbonded pdb=" OG SER E 275 " pdb="MG MG E 802 " model vdw 2.069 2.170 nonbonded pdb=" OG SER B 275 " pdb="MG MG B 802 " model vdw 2.070 2.170 nonbonded pdb=" O2B AGS E 801 " pdb="MG MG E 802 " model vdw 2.089 2.170 ... (remaining 81649 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 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 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 : 0.006 0.061 11362 Z= 0.260 Angle : 1.003 8.618 15516 Z= 0.536 Chirality : 0.051 0.235 1738 Planarity : 0.007 0.048 1980 Dihedral : 14.632 162.297 4108 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 2.17 % Allowed : 17.66 % Favored : 80.17 % Rotamer: Outliers : 1.02 % Allowed : 4.32 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.30 (0.18), residues: 1382 helix: -2.03 (0.16), residues: 470 sheet: -1.32 (0.34), residues: 212 loop : -4.10 (0.19), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 156 TYR 0.022 0.002 TYR B 685 PHE 0.017 0.002 PHE E 139 TRP 0.029 0.002 TRP E 297 HIS 0.005 0.001 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (11362) covalent geometry : angle 1.00268 / 0.54 (15516) hydrogen bonds : bond 0.16223 / 11.22 ( 496) hydrogen bonds : angle 7.03863 / 5.23 ( 1470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 371 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 VAL cc_start: 0.6082 (t) cc_final: 0.5842 (t) REVERT: B 154 VAL cc_start: 0.4398 (OUTLIER) cc_final: 0.4036 (m) REVERT: E 154 VAL cc_start: 0.3642 (OUTLIER) cc_final: 0.3333 (m) REVERT: E 354 VAL cc_start: 0.6110 (t) cc_final: 0.5699 (t) outliers start: 12 outliers final: 3 residues processed: 378 average time/residue: 0.4618 time to fit residues: 191.5011 Evaluate side-chains 216 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 211 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 249 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN A 143 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 174 HIS B 283 ASN B 480 GLN D 21 GLN D 143 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 174 HIS E 334 HIS E 480 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095838 restraints weight = 17266.576| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.15 r_work: 0.3182 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11362 Z= 0.202 Angle : 0.916 12.726 15516 Z= 0.447 Chirality : 0.048 0.204 1738 Planarity : 0.008 0.062 1980 Dihedral : 8.983 164.938 1554 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 4.83 % Allowed : 16.78 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.10 (0.22), residues: 1382 helix: 1.92 (0.22), residues: 478 sheet: -0.65 (0.36), residues: 188 loop : -2.81 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 160 TYR 0.017 0.002 TYR E 685 PHE 0.040 0.003 PHE B 332 TRP 0.042 0.002 TRP A 171 HIS 0.011 0.002 HIS E 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (11362) covalent geometry : angle 0.91643 / 0.45 (15516) hydrogen bonds : bond 0.05091 / 3.50 ( 496) hydrogen bonds : angle 4.73355 / 3.56 ( 1470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.6357 (tt0) REVERT: B 190 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6626 (mt-10) REVERT: B 353 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6457 (t) REVERT: B 389 GLU cc_start: 0.7287 (pt0) cc_final: 0.6519 (pp20) REVERT: B 559 LEU cc_start: 0.7034 (pp) cc_final: 0.6802 (mt) REVERT: D 14 GLU cc_start: 0.7774 (tp30) cc_final: 0.7349 (mm-30) REVERT: E 202 GLU cc_start: 0.8022 (tt0) cc_final: 0.7533 (tm-30) REVERT: E 306 ASP cc_start: 0.6876 (t70) cc_final: 0.6393 (t0) REVERT: E 364 PRO cc_start: 0.6452 (Cg_exo) cc_final: 0.6149 (Cg_endo) REVERT: E 389 GLU cc_start: 0.7354 (pt0) cc_final: 0.6492 (pp20) REVERT: E 687 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7623 (ttpp) outliers start: 57 outliers final: 19 residues processed: 295 average time/residue: 0.3970 time to fit residues: 130.0419 Evaluate side-chains 237 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 687 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 38 optimal weight: 0.1980 chunk 117 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 chunk 96 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 174 HIS B 246 ASN B 283 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN D 21 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.118723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096499 restraints weight = 17613.946| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.16 r_work: 0.3212 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11362 Z= 0.138 Angle : 0.761 10.896 15516 Z= 0.364 Chirality : 0.043 0.176 1738 Planarity : 0.006 0.050 1980 Dihedral : 8.671 163.631 1546 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.49 % Allowed : 21.86 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1382 helix: 2.79 (0.22), residues: 488 sheet: -0.56 (0.35), residues: 206 loop : -2.55 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 201 TYR 0.020 0.001 TYR D 170 PHE 0.023 0.002 PHE B 139 TRP 0.019 0.001 TRP A 347 HIS 0.011 0.001 HIS B 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (11362) covalent geometry : angle 0.76068 / 0.36 (15516) hydrogen bonds : bond 0.04565 / 3.13 ( 496) hydrogen bonds : angle 4.38172 / 3.30 ( 1470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5662 (tpp) cc_final: 0.4443 (mmt) REVERT: A 21 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: A 62 GLN cc_start: 0.8448 (tt0) cc_final: 0.8233 (tt0) REVERT: B 251 GLU cc_start: 0.8417 (tt0) cc_final: 0.7851 (pt0) REVERT: B 353 THR cc_start: 0.7181 (OUTLIER) cc_final: 0.6911 (t) REVERT: B 389 GLU cc_start: 0.7174 (pt0) cc_final: 0.6498 (pp20) REVERT: B 477 MET cc_start: 0.7721 (mmt) cc_final: 0.7445 (mtm) REVERT: B 613 LEU cc_start: 0.8324 (pt) cc_final: 0.7825 (tp) REVERT: D 14 GLU cc_start: 0.7917 (tp30) cc_final: 0.7519 (mm-30) REVERT: D 349 LEU cc_start: 0.7946 (tp) cc_final: 0.7712 (tt) REVERT: E 202 GLU cc_start: 0.8108 (tt0) cc_final: 0.7743 (tm-30) REVERT: E 251 GLU cc_start: 0.8409 (tt0) cc_final: 0.7792 (pt0) REVERT: E 318 VAL cc_start: 0.7380 (m) cc_final: 0.7144 (m) REVERT: E 353 THR cc_start: 0.6772 (OUTLIER) cc_final: 0.6542 (t) REVERT: E 364 PRO cc_start: 0.6438 (Cg_exo) cc_final: 0.6192 (Cg_endo) REVERT: E 389 GLU cc_start: 0.7144 (pt0) cc_final: 0.6395 (pp20) REVERT: E 567 ASP cc_start: 0.4229 (OUTLIER) cc_final: 0.3985 (p0) outliers start: 53 outliers final: 20 residues processed: 262 average time/residue: 0.3723 time to fit residues: 108.9012 Evaluate side-chains 221 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 567 ASP Chi-restraints excluded: chain E residue 653 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 0.0870 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 327 ASN B 334 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B 532 HIS ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN E 327 ASN E 334 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092282 restraints weight = 17661.079| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.18 r_work: 0.3136 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.9160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.177 11362 Z= 0.304 Angle : 0.935 11.031 15516 Z= 0.474 Chirality : 0.051 0.250 1738 Planarity : 0.007 0.054 1980 Dihedral : 8.803 154.401 1546 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 5.76 % Allowed : 22.12 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.22), residues: 1382 helix: 1.56 (0.21), residues: 490 sheet: -0.71 (0.35), residues: 220 loop : -2.33 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 205 TYR 0.021 0.003 TYR E 423 PHE 0.042 0.003 PHE D 107 TRP 0.045 0.003 TRP A 171 HIS 0.018 0.003 HIS E 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.30 (11362) covalent geometry : angle 0.93538 / 0.47 (15516) hydrogen bonds : bond 0.07221 / 4.88 ( 496) hydrogen bonds : angle 4.83413 / 3.65 ( 1470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 277 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8631 (m-80) cc_final: 0.8421 (m-80) REVERT: B 132 SER cc_start: 0.7255 (OUTLIER) cc_final: 0.7029 (p) REVERT: B 151 GLN cc_start: 0.8366 (tt0) cc_final: 0.7700 (tt0) REVERT: B 190 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: B 200 LEU cc_start: 0.8833 (tp) cc_final: 0.8622 (tp) REVERT: B 251 GLU cc_start: 0.8546 (tt0) cc_final: 0.7985 (pt0) REVERT: B 483 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: B 525 LEU cc_start: 0.8256 (tp) cc_final: 0.7864 (tt) REVERT: B 534 TYR cc_start: 0.8291 (m-80) cc_final: 0.8080 (m-80) REVERT: B 560 ARG cc_start: 0.7580 (tmm-80) cc_final: 0.7375 (ttp80) REVERT: B 626 TYR cc_start: 0.8266 (m-80) cc_final: 0.8025 (m-80) REVERT: D 21 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: D 62 GLN cc_start: 0.8746 (tp40) cc_final: 0.8320 (tp40) REVERT: E 151 GLN cc_start: 0.8324 (tt0) cc_final: 0.7806 (tt0) REVERT: E 187 THR cc_start: 0.7468 (m) cc_final: 0.7245 (p) REVERT: E 200 LEU cc_start: 0.8996 (tp) cc_final: 0.8760 (tp) REVERT: E 251 GLU cc_start: 0.8541 (tt0) cc_final: 0.7907 (pt0) REVERT: E 377 ASP cc_start: 0.8394 (t70) cc_final: 0.7865 (t70) REVERT: E 425 SER cc_start: 0.8675 (m) cc_final: 0.7860 (t) REVERT: E 560 ARG cc_start: 0.7635 (tmm-80) cc_final: 0.7281 (ttp80) REVERT: E 626 TYR cc_start: 0.8256 (m-80) cc_final: 0.7916 (m-80) outliers start: 68 outliers final: 20 residues processed: 327 average time/residue: 0.4292 time to fit residues: 154.6993 Evaluate side-chains 216 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 639 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 564 VAL Chi-restraints excluded: chain E residue 653 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 132 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 334 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN D 21 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS E 222 GLN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091808 restraints weight = 17481.955| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.11 r_work: 0.3119 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.9633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11362 Z= 0.160 Angle : 0.765 8.012 15516 Z= 0.372 Chirality : 0.044 0.211 1738 Planarity : 0.006 0.047 1980 Dihedral : 8.467 155.729 1546 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.75 % Allowed : 27.97 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1382 helix: 2.47 (0.23), residues: 480 sheet: -0.67 (0.33), residues: 230 loop : -2.14 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 257 TYR 0.013 0.002 TYR B 626 PHE 0.019 0.002 PHE B 312 TRP 0.009 0.001 TRP D 168 HIS 0.007 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (11362) covalent geometry : angle 0.76548 / 0.37 (15516) hydrogen bonds : bond 0.04872 / 3.34 ( 496) hydrogen bonds : angle 4.32738 / 3.27 ( 1470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.440 Fit side-chains REVERT: A 1 MET cc_start: 0.6265 (tpp) cc_final: 0.4827 (mmt) REVERT: B 131 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7409 (pp) REVERT: B 151 GLN cc_start: 0.8342 (tt0) cc_final: 0.7956 (tt0) REVERT: B 174 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7698 (t-90) REVERT: B 190 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: B 200 LEU cc_start: 0.8948 (tp) cc_final: 0.8724 (tp) REVERT: B 251 GLU cc_start: 0.8566 (tt0) cc_final: 0.8074 (pt0) REVERT: B 313 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8497 (m) REVERT: B 430 GLU cc_start: 0.8221 (tp30) cc_final: 0.7941 (tp30) REVERT: B 446 ILE cc_start: 0.8826 (mt) cc_final: 0.8613 (mm) REVERT: B 485 LEU cc_start: 0.8917 (tt) cc_final: 0.8684 (tp) REVERT: B 525 LEU cc_start: 0.8417 (tp) cc_final: 0.8078 (tt) REVERT: B 560 ARG cc_start: 0.7596 (tmm-80) cc_final: 0.7353 (ttp80) REVERT: B 626 TYR cc_start: 0.8220 (m-80) cc_final: 0.7777 (m-80) REVERT: D 62 GLN cc_start: 0.8588 (tp40) cc_final: 0.8352 (tp40) REVERT: D 129 LYS cc_start: 0.8683 (tppt) cc_final: 0.8418 (ttpp) REVERT: D 349 LEU cc_start: 0.9184 (tt) cc_final: 0.8897 (tm) REVERT: E 131 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7439 (pp) REVERT: E 200 LEU cc_start: 0.8996 (tp) cc_final: 0.8745 (tp) REVERT: E 251 GLU cc_start: 0.8568 (tt0) cc_final: 0.8045 (pt0) REVERT: E 394 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8530 (m) REVERT: E 407 ASP cc_start: 0.8790 (t0) cc_final: 0.8568 (m-30) REVERT: E 623 SER cc_start: 0.9082 (t) cc_final: 0.8649 (p) REVERT: E 626 TYR cc_start: 0.8151 (m-80) cc_final: 0.7811 (m-80) outliers start: 56 outliers final: 16 residues processed: 274 average time/residue: 0.4529 time to fit residues: 135.5524 Evaluate side-chains 227 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 480 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN E 115 GLN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089868 restraints weight = 17601.234| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.11 r_work: 0.3082 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 1.0020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 11362 Z= 0.169 Angle : 0.745 8.723 15516 Z= 0.363 Chirality : 0.044 0.168 1738 Planarity : 0.006 0.076 1980 Dihedral : 8.307 153.668 1546 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.32 % Allowed : 29.24 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1382 helix: 2.60 (0.23), residues: 480 sheet: -0.79 (0.33), residues: 236 loop : -1.89 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 560 TYR 0.027 0.002 TYR E 382 PHE 0.027 0.002 PHE B 312 TRP 0.009 0.001 TRP B 400 HIS 0.006 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (11362) covalent geometry : angle 0.74470 / 0.36 (15516) hydrogen bonds : bond 0.04926 / 3.37 ( 496) hydrogen bonds : angle 4.17934 / 3.15 ( 1470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 211 time to evaluate : 0.436 Fit side-chains REVERT: A 139 GLU cc_start: 0.8831 (tt0) cc_final: 0.8620 (tt0) REVERT: B 131 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7364 (pp) REVERT: B 151 GLN cc_start: 0.8367 (tt0) cc_final: 0.7974 (tt0) REVERT: B 174 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7682 (t-90) REVERT: B 190 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: B 200 LEU cc_start: 0.9012 (tp) cc_final: 0.8807 (tp) REVERT: B 205 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8607 (ttm110) REVERT: B 251 GLU cc_start: 0.8509 (tt0) cc_final: 0.7998 (pt0) REVERT: B 309 GLN cc_start: 0.8666 (tt0) cc_final: 0.8446 (tt0) REVERT: B 313 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8461 (m) REVERT: B 401 ILE cc_start: 0.8752 (pt) cc_final: 0.8482 (pt) REVERT: B 407 ASP cc_start: 0.8819 (t0) cc_final: 0.8591 (m-30) REVERT: B 446 ILE cc_start: 0.8850 (mt) cc_final: 0.8625 (mm) REVERT: B 525 LEU cc_start: 0.8487 (tp) cc_final: 0.8134 (tt) REVERT: B 560 ARG cc_start: 0.7649 (tmm-80) cc_final: 0.7383 (ttp80) REVERT: B 644 ASN cc_start: 0.7420 (m-40) cc_final: 0.6869 (p0) REVERT: D 62 GLN cc_start: 0.8663 (tp40) cc_final: 0.8393 (tp40) REVERT: D 129 LYS cc_start: 0.8684 (tppt) cc_final: 0.8450 (ttpp) REVERT: D 349 LEU cc_start: 0.9248 (tt) cc_final: 0.8975 (tm) REVERT: E 131 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7385 (pp) REVERT: E 200 LEU cc_start: 0.9060 (tp) cc_final: 0.8797 (tp) REVERT: E 251 GLU cc_start: 0.8556 (tt0) cc_final: 0.8049 (pt0) REVERT: E 309 GLN cc_start: 0.8660 (tt0) cc_final: 0.8418 (tt0) REVERT: E 313 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8353 (m) REVERT: E 320 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7098 (pt) REVERT: E 394 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8562 (m) REVERT: E 407 ASP cc_start: 0.8818 (t0) cc_final: 0.8612 (m-30) REVERT: E 623 SER cc_start: 0.9117 (t) cc_final: 0.8675 (p) REVERT: E 626 TYR cc_start: 0.8249 (m-80) cc_final: 0.7801 (m-80) outliers start: 51 outliers final: 20 residues processed: 247 average time/residue: 0.4383 time to fit residues: 119.0138 Evaluate side-chains 227 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 103 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 47 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS B 334 HIS B 689 ASN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.113551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091955 restraints weight = 17297.563| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.00 r_work: 0.3122 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 1.0238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11362 Z= 0.128 Angle : 0.714 9.997 15516 Z= 0.343 Chirality : 0.042 0.150 1738 Planarity : 0.006 0.067 1980 Dihedral : 8.193 154.133 1546 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.07 % Allowed : 29.75 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1382 helix: 2.87 (0.23), residues: 480 sheet: -0.33 (0.37), residues: 194 loop : -1.75 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 560 TYR 0.024 0.001 TYR E 382 PHE 0.029 0.002 PHE B 312 TRP 0.011 0.001 TRP D 168 HIS 0.004 0.001 HIS E 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (11362) covalent geometry : angle 0.71362 / 0.34 (15516) hydrogen bonds : bond 0.04133 / 2.83 ( 496) hydrogen bonds : angle 3.98874 / 3.00 ( 1470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.391 Fit side-chains REVERT: A 62 GLN cc_start: 0.8725 (tp40) cc_final: 0.8396 (tt0) REVERT: A 139 GLU cc_start: 0.8856 (tt0) cc_final: 0.8641 (tt0) REVERT: A 141 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8233 (tmm-80) REVERT: B 131 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7289 (pp) REVERT: B 174 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7651 (t-90) REVERT: B 190 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6548 (mp0) REVERT: B 200 LEU cc_start: 0.9020 (tp) cc_final: 0.8807 (tp) REVERT: B 205 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8480 (ttp-110) REVERT: B 251 GLU cc_start: 0.8496 (tt0) cc_final: 0.8047 (pt0) REVERT: B 309 GLN cc_start: 0.8606 (tt0) cc_final: 0.8343 (tt0) REVERT: B 313 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8364 (m) REVERT: B 394 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8680 (m) REVERT: B 446 ILE cc_start: 0.8701 (mt) cc_final: 0.8494 (mm) REVERT: B 525 LEU cc_start: 0.8474 (tp) cc_final: 0.8115 (tt) REVERT: B 560 ARG cc_start: 0.7956 (tmm-80) cc_final: 0.7533 (ttp80) REVERT: B 644 ASN cc_start: 0.7471 (m-40) cc_final: 0.6898 (p0) REVERT: D 62 GLN cc_start: 0.8541 (tp40) cc_final: 0.8236 (tp40) REVERT: D 129 LYS cc_start: 0.8691 (tppt) cc_final: 0.8487 (ttpm) REVERT: D 349 LEU cc_start: 0.9230 (tt) cc_final: 0.8940 (tm) REVERT: E 131 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7323 (pp) REVERT: E 200 LEU cc_start: 0.9060 (tp) cc_final: 0.8762 (tp) REVERT: E 251 GLU cc_start: 0.8546 (tt0) cc_final: 0.8070 (pt0) REVERT: E 309 GLN cc_start: 0.8646 (tt0) cc_final: 0.8426 (tt0) REVERT: E 313 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8274 (m) REVERT: E 394 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8554 (m) REVERT: E 401 ILE cc_start: 0.8713 (pt) cc_final: 0.8424 (pt) REVERT: E 623 SER cc_start: 0.9081 (t) cc_final: 0.8602 (p) outliers start: 48 outliers final: 19 residues processed: 237 average time/residue: 0.4965 time to fit residues: 128.4830 Evaluate side-chains 221 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 242 HIS Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 684 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 689 ASN D 3 GLN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087207 restraints weight = 17510.508| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.06 r_work: 0.3035 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 1.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11362 Z= 0.201 Angle : 0.762 10.805 15516 Z= 0.368 Chirality : 0.045 0.161 1738 Planarity : 0.006 0.071 1980 Dihedral : 8.151 152.879 1546 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.73 % Allowed : 29.92 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.24), residues: 1382 helix: 2.64 (0.23), residues: 492 sheet: -0.32 (0.38), residues: 196 loop : -1.81 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 201 TYR 0.025 0.002 TYR B 382 PHE 0.031 0.002 PHE B 312 TRP 0.012 0.001 TRP B 400 HIS 0.005 0.001 HIS E 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (11362) covalent geometry : angle 0.76232 / 0.37 (15516) hydrogen bonds : bond 0.05500 / 3.72 ( 496) hydrogen bonds : angle 4.18135 / 3.15 ( 1470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 131 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7450 (pp) REVERT: B 174 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7607 (t-90) REVERT: B 205 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8499 (ttm-80) REVERT: B 251 GLU cc_start: 0.8526 (tt0) cc_final: 0.8081 (pt0) REVERT: B 259 LYS cc_start: 0.6896 (OUTLIER) cc_final: 0.6597 (ttpt) REVERT: B 313 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8448 (m) REVERT: B 394 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8612 (m) REVERT: B 446 ILE cc_start: 0.8849 (mt) cc_final: 0.8605 (mm) REVERT: B 525 LEU cc_start: 0.8480 (tp) cc_final: 0.8111 (tt) REVERT: B 557 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: B 560 ARG cc_start: 0.8040 (tmm-80) cc_final: 0.7551 (ttp80) REVERT: B 623 SER cc_start: 0.9082 (t) cc_final: 0.8872 (t) REVERT: B 626 TYR cc_start: 0.7892 (m-80) cc_final: 0.7529 (m-80) REVERT: B 644 ASN cc_start: 0.7499 (m-40) cc_final: 0.7075 (p0) REVERT: D 23 TYR cc_start: 0.8773 (m-80) cc_final: 0.8333 (m-80) REVERT: D 62 GLN cc_start: 0.8728 (tp40) cc_final: 0.8434 (tp40) REVERT: D 129 LYS cc_start: 0.8814 (tppt) cc_final: 0.8587 (ttpm) REVERT: E 131 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7450 (pp) REVERT: E 251 GLU cc_start: 0.8520 (tt0) cc_final: 0.8083 (pt0) REVERT: E 309 GLN cc_start: 0.8734 (tt0) cc_final: 0.8237 (mt0) REVERT: E 313 SER cc_start: 0.8853 (OUTLIER) cc_final: 0.8356 (m) REVERT: E 320 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.6999 (pt) REVERT: E 394 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8498 (m) REVERT: E 557 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: E 623 SER cc_start: 0.9102 (t) cc_final: 0.8865 (t) REVERT: E 626 TYR cc_start: 0.7894 (m-80) cc_final: 0.7642 (m-80) REVERT: E 644 ASN cc_start: 0.7649 (m-40) cc_final: 0.7191 (m110) outliers start: 44 outliers final: 19 residues processed: 228 average time/residue: 0.4521 time to fit residues: 112.8159 Evaluate side-chains 211 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 141 ARG Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 557 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 3 GLN A 62 GLN B 334 HIS B 689 ASN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.111261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089483 restraints weight = 17301.625| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.07 r_work: 0.3080 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 1.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11362 Z= 0.139 Angle : 0.725 11.882 15516 Z= 0.347 Chirality : 0.043 0.150 1738 Planarity : 0.006 0.068 1980 Dihedral : 8.103 153.403 1546 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.81 % Allowed : 30.51 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.23), residues: 1382 helix: 2.66 (0.23), residues: 492 sheet: -0.29 (0.37), residues: 196 loop : -1.74 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 201 TYR 0.019 0.002 TYR B 382 PHE 0.031 0.002 PHE E 312 TRP 0.011 0.001 TRP D 168 HIS 0.006 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11362) covalent geometry : angle 0.72528 / 0.35 (15516) hydrogen bonds : bond 0.04472 / 3.04 ( 496) hydrogen bonds : angle 4.04717 / 3.06 ( 1470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: A 141 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8042 (tmm-80) REVERT: A 362 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8938 (pt) REVERT: B 131 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7407 (pp) REVERT: B 151 GLN cc_start: 0.8301 (tt0) cc_final: 0.8088 (tm-30) REVERT: B 165 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: B 174 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7638 (t-90) REVERT: B 205 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8587 (ttp-110) REVERT: B 251 GLU cc_start: 0.8516 (tt0) cc_final: 0.8118 (pt0) REVERT: B 313 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8458 (m) REVERT: B 394 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8604 (m) REVERT: B 525 LEU cc_start: 0.8522 (tp) cc_final: 0.8158 (tt) REVERT: B 557 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: B 560 ARG cc_start: 0.8170 (tmm-80) cc_final: 0.7681 (ttp80) REVERT: B 623 SER cc_start: 0.9070 (t) cc_final: 0.8792 (t) REVERT: B 626 TYR cc_start: 0.7920 (m-80) cc_final: 0.7690 (m-80) REVERT: B 644 ASN cc_start: 0.7510 (m-40) cc_final: 0.7114 (p0) REVERT: D 23 TYR cc_start: 0.8792 (m-80) cc_final: 0.8252 (m-80) REVERT: D 62 GLN cc_start: 0.8569 (tp40) cc_final: 0.8321 (tp40) REVERT: D 129 LYS cc_start: 0.8808 (tppt) cc_final: 0.8599 (ttpm) REVERT: D 352 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8298 (mt-10) REVERT: D 362 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8931 (pt) REVERT: E 131 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7442 (pp) REVERT: E 206 LEU cc_start: 0.8932 (mt) cc_final: 0.8700 (mp) REVERT: E 251 GLU cc_start: 0.8501 (tt0) cc_final: 0.8156 (pt0) REVERT: E 309 GLN cc_start: 0.8692 (tt0) cc_final: 0.8220 (mt0) REVERT: E 313 SER cc_start: 0.8840 (OUTLIER) cc_final: 0.8358 (m) REVERT: E 394 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (m) REVERT: E 401 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8616 (pp) REVERT: E 557 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7110 (pp20) REVERT: E 623 SER cc_start: 0.9075 (t) cc_final: 0.8869 (t) REVERT: E 626 TYR cc_start: 0.7926 (m-80) cc_final: 0.7707 (m-80) REVERT: E 644 ASN cc_start: 0.7668 (m-40) cc_final: 0.7229 (m-40) outliers start: 45 outliers final: 12 residues processed: 217 average time/residue: 0.4444 time to fit residues: 105.4877 Evaluate side-chains 203 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 396 ASN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 0.0000 chunk 124 optimal weight: 0.8980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 480 GLN B 689 ASN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS E 689 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089900 restraints weight = 17625.290| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.07 r_work: 0.3085 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 1.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11362 Z= 0.138 Angle : 0.734 12.396 15516 Z= 0.349 Chirality : 0.043 0.209 1738 Planarity : 0.006 0.066 1980 Dihedral : 8.058 152.826 1546 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.22 % Allowed : 30.85 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1382 helix: 2.72 (0.23), residues: 492 sheet: -0.28 (0.37), residues: 196 loop : -1.74 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 201 TYR 0.027 0.001 TYR E 382 PHE 0.031 0.002 PHE E 312 TRP 0.013 0.001 TRP B 297 HIS 0.007 0.001 HIS B 532 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11362) covalent geometry : angle 0.73412 / 0.35 (15516) hydrogen bonds : bond 0.04294 / 2.92 ( 496) hydrogen bonds : angle 4.00757 / 3.02 ( 1470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8027 (tmm-80) REVERT: A 362 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8960 (pt) REVERT: B 131 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7355 (pp) REVERT: B 165 ASP cc_start: 0.8076 (t0) cc_final: 0.7799 (m-30) REVERT: B 174 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7613 (t-90) REVERT: B 202 GLU cc_start: 0.8672 (tt0) cc_final: 0.8369 (tp30) REVERT: B 206 LEU cc_start: 0.8580 (tt) cc_final: 0.8259 (tt) REVERT: B 251 GLU cc_start: 0.8489 (tt0) cc_final: 0.8109 (pt0) REVERT: B 309 GLN cc_start: 0.8564 (tt0) cc_final: 0.8250 (mt0) REVERT: B 313 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8452 (m) REVERT: B 394 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8575 (m) REVERT: B 525 LEU cc_start: 0.8526 (tp) cc_final: 0.8140 (tt) REVERT: B 557 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7078 (pp20) REVERT: B 560 ARG cc_start: 0.8154 (tmm-80) cc_final: 0.7691 (ttp80) REVERT: B 623 SER cc_start: 0.9056 (t) cc_final: 0.8751 (t) REVERT: B 626 TYR cc_start: 0.7894 (m-80) cc_final: 0.7613 (m-80) REVERT: B 644 ASN cc_start: 0.7514 (m-40) cc_final: 0.7113 (p0) REVERT: D 23 TYR cc_start: 0.8790 (m-80) cc_final: 0.8225 (m-80) REVERT: D 62 GLN cc_start: 0.8562 (tp40) cc_final: 0.8325 (tp40) REVERT: D 362 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8941 (pt) REVERT: E 251 GLU cc_start: 0.8496 (tt0) cc_final: 0.8158 (pt0) REVERT: E 313 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8320 (m) REVERT: E 394 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8555 (m) REVERT: E 401 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8604 (pp) REVERT: E 557 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7179 (pp20) REVERT: E 623 SER cc_start: 0.9056 (t) cc_final: 0.8795 (t) REVERT: E 644 ASN cc_start: 0.7674 (m-40) cc_final: 0.7231 (m-40) outliers start: 38 outliers final: 16 residues processed: 210 average time/residue: 0.4832 time to fit residues: 110.5530 Evaluate side-chains 204 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 353 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 353 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 396 ASN Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 689 ASN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090120 restraints weight = 17482.737| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.07 r_work: 0.3092 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 1.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11362 Z= 0.135 Angle : 0.728 12.849 15516 Z= 0.346 Chirality : 0.043 0.225 1738 Planarity : 0.006 0.062 1980 Dihedral : 8.003 152.899 1546 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.97 % Allowed : 31.27 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1382 helix: 2.81 (0.23), residues: 490 sheet: -0.35 (0.35), residues: 210 loop : -1.79 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 201 TYR 0.029 0.001 TYR E 382 PHE 0.030 0.002 PHE E 312 TRP 0.013 0.001 TRP D 168 HIS 0.007 0.001 HIS B 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11362) covalent geometry : angle 0.72775 / 0.35 (15516) hydrogen bonds : bond 0.04224 / 2.88 ( 496) hydrogen bonds : angle 3.99211 / 3.00 ( 1470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3330.73 seconds wall clock time: 57 minutes 32.93 seconds (3452.93 seconds total)