Starting phenix.real_space_refine on Wed Mar 4 05:24:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6of2_20040/03_2026/6of2_20040.cif Found real_map, /net/cci-nas-00/data/ceres_data/6of2_20040/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6of2_20040/03_2026/6of2_20040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6of2_20040/03_2026/6of2_20040.map" model { file = "/net/cci-nas-00/data/ceres_data/6of2_20040/03_2026/6of2_20040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6of2_20040/03_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-dev-5986/lib/python3.9/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: 3.67, per 1000 atoms: 0.33 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: 0.93 Conformation dependent library (CDL) restraints added in 533.5 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: 0.35 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: 1.79 Time building geometry restraints manager: 1.25 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: 6592 32.46 - 64.92: 184 64.92 - 97.38: 4 97.38 - 129.84: 0 129.84 - 162.30: 2 Dihedral angle restraints: 6782 sinusoidal: 2690 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 6779 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 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 : 14.668 162.297 4130 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 covalent geometry : bond 0.00590 (11362) covalent geometry : angle 1.00268 (15516) hydrogen bonds : bond 0.16223 ( 496) hydrogen bonds : angle 7.03863 ( 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 : 0.403 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: 0.4727 time to fit residues: 195.4593 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... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 143 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 174 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN D 21 GLN D 143 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 144 ASN E 174 HIS ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 HIS E 480 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.118749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096516 restraints weight = 17245.230| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.15 r_work: 0.3193 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.4125 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= 0.194 Angle : 0.923 12.406 15516 Z= 0.449 Chirality : 0.049 0.191 1738 Planarity : 0.008 0.062 1980 Dihedral : 9.327 161.557 1576 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.49 % Allowed : 16.95 % Favored : 78.56 % 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: -1.09 (0.22), residues: 1382 helix: 1.87 (0.22), residues: 478 sheet: -0.62 (0.36), residues: 188 loop : -2.77 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 160 TYR 0.017 0.002 TYR B 482 PHE 0.037 0.003 PHE B 332 TRP 0.034 0.002 TRP A 171 HIS 0.011 0.002 HIS E 484 Details of bonding type rmsd covalent geometry : bond 0.00424 (11362) covalent geometry : angle 0.92318 (15516) hydrogen bonds : bond 0.04990 ( 496) hydrogen bonds : angle 4.70568 ( 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 310 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6556 (tt0) REVERT: A 75 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7148 (mm) REVERT: B 389 GLU cc_start: 0.7264 (pt0) cc_final: 0.6506 (pp20) REVERT: B 559 LEU cc_start: 0.7072 (pp) cc_final: 0.6805 (mt) REVERT: D 14 GLU cc_start: 0.7831 (tp30) cc_final: 0.7424 (mm-30) REVERT: E 202 GLU cc_start: 0.8074 (tt0) cc_final: 0.7593 (tm-30) REVERT: E 306 ASP cc_start: 0.6967 (t70) cc_final: 0.6522 (t0) REVERT: E 318 VAL cc_start: 0.7442 (m) cc_final: 0.7183 (m) REVERT: E 364 PRO cc_start: 0.6565 (Cg_exo) cc_final: 0.6260 (Cg_endo) REVERT: E 389 GLU cc_start: 0.7346 (pt0) cc_final: 0.6485 (pp20) REVERT: E 687 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7657 (ttpp) outliers start: 53 outliers final: 14 residues processed: 292 average time/residue: 0.4101 time to fit residues: 132.6851 Evaluate side-chains 239 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 449 THR Chi-restraints excluded: chain E residue 470 THR 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: 0.0870 chunk 117 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 138 optimal weight: 0.7980 chunk 96 optimal weight: 0.0270 chunk 31 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 132 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN B 174 HIS B 283 ASN B 480 GLN D 21 GLN ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN E 207 ASN E 246 ASN E 334 HIS ** E 544 ASN ** 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 = 0.3666 r_free = 0.3666 target = 0.119968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097965 restraints weight = 17593.081| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.16 r_work: 0.3225 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11362 Z= 0.128 Angle : 0.756 10.851 15516 Z= 0.361 Chirality : 0.043 0.191 1738 Planarity : 0.006 0.050 1980 Dihedral : 8.916 159.450 1568 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 4.32 % Allowed : 21.86 % Favored : 73.81 % 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: -0.21 (0.23), residues: 1382 helix: 2.96 (0.22), residues: 478 sheet: -0.51 (0.35), residues: 206 loop : -2.44 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 201 TYR 0.021 0.001 TYR D 170 PHE 0.023 0.001 PHE B 139 TRP 0.016 0.001 TRP A 347 HIS 0.012 0.001 HIS B 174 Details of bonding type rmsd covalent geometry : bond 0.00272 (11362) covalent geometry : angle 0.75622 (15516) hydrogen bonds : bond 0.04339 ( 496) hydrogen bonds : angle 4.31903 ( 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 273 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: B 251 GLU cc_start: 0.8376 (tt0) cc_final: 0.7770 (pt0) REVERT: B 283 ASN cc_start: 0.6643 (m-40) cc_final: 0.6440 (m110) REVERT: B 389 GLU cc_start: 0.7138 (pt0) cc_final: 0.6484 (pp20) REVERT: B 477 MET cc_start: 0.7994 (mtp) cc_final: 0.7595 (mmt) REVERT: B 532 HIS cc_start: 0.7393 (t-90) cc_final: 0.7062 (t-90) REVERT: D 14 GLU cc_start: 0.7922 (tp30) cc_final: 0.7606 (tt0) REVERT: D 349 LEU cc_start: 0.7892 (tp) cc_final: 0.7658 (tt) REVERT: E 202 GLU cc_start: 0.8072 (tt0) cc_final: 0.7752 (tm-30) REVERT: E 251 GLU cc_start: 0.8351 (tt0) cc_final: 0.7730 (pt0) REVERT: E 318 VAL cc_start: 0.7248 (m) cc_final: 0.6959 (m) REVERT: E 364 PRO cc_start: 0.6372 (Cg_exo) cc_final: 0.6126 (Cg_endo) REVERT: E 389 GLU cc_start: 0.7210 (pt0) cc_final: 0.6435 (pp20) outliers start: 51 outliers final: 19 residues processed: 256 average time/residue: 0.4037 time to fit residues: 114.6962 Evaluate side-chains 219 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE 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 180 VAL 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 76 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE 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 653 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 28 optimal weight: 0.0170 chunk 54 optimal weight: 0.0060 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS E 115 GLN E 207 ASN E 246 ASN ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 533 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.115878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093829 restraints weight = 17623.124| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.19 r_work: 0.3157 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.9321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11362 Z= 0.276 Angle : 0.943 10.657 15516 Z= 0.471 Chirality : 0.051 0.260 1738 Planarity : 0.008 0.064 1980 Dihedral : 9.329 150.531 1568 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 6.10 % Allowed : 21.44 % Favored : 72.46 % 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: -0.89 (0.22), residues: 1382 helix: 1.55 (0.21), residues: 490 sheet: -0.86 (0.34), residues: 220 loop : -2.23 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 201 TYR 0.020 0.003 TYR E 423 PHE 0.044 0.003 PHE A 107 TRP 0.043 0.003 TRP A 171 HIS 0.024 0.003 HIS E 334 Details of bonding type rmsd covalent geometry : bond 0.00627 (11362) covalent geometry : angle 0.94319 (15516) hydrogen bonds : bond 0.07301 ( 496) hydrogen bonds : angle 4.82693 ( 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 358 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6233 (tpp) cc_final: 0.6033 (OUTLIER) REVERT: A 352 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8480 (mp0) REVERT: B 151 GLN cc_start: 0.8311 (tt0) cc_final: 0.7762 (tt0) REVERT: B 187 THR cc_start: 0.7365 (m) cc_final: 0.7077 (p) REVERT: B 200 LEU cc_start: 0.8891 (tp) cc_final: 0.8673 (tp) REVERT: B 251 GLU cc_start: 0.8539 (tt0) cc_final: 0.8038 (pt0) REVERT: B 525 LEU cc_start: 0.8154 (tp) cc_final: 0.7777 (tt) REVERT: B 560 ARG cc_start: 0.7588 (tmm-80) cc_final: 0.7376 (ttp80) REVERT: B 626 TYR cc_start: 0.8194 (m-80) cc_final: 0.7991 (m-80) REVERT: D 15 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8512 (tp) REVERT: D 354 GLU cc_start: 0.7813 (tp30) cc_final: 0.7490 (tp30) REVERT: E 151 GLN cc_start: 0.8363 (tt0) cc_final: 0.7736 (tt0) REVERT: E 200 LEU cc_start: 0.9006 (tp) cc_final: 0.8767 (tp) REVERT: E 251 GLU cc_start: 0.8538 (tt0) cc_final: 0.7940 (pt0) REVERT: E 377 ASP cc_start: 0.8374 (t0) cc_final: 0.7965 (t0) REVERT: E 425 SER cc_start: 0.8655 (m) cc_final: 0.7857 (t) REVERT: E 560 ARG cc_start: 0.7685 (tmm-80) cc_final: 0.7310 (ttp80) REVERT: E 623 SER cc_start: 0.9136 (t) cc_final: 0.8813 (p) outliers start: 72 outliers final: 17 residues processed: 338 average time/residue: 0.4841 time to fit residues: 178.9371 Evaluate side-chains 225 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 205 ARG 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 D residue 1 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 335 PRO Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 470 THR 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: 0.7980 chunk 89 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 222 GLN B 327 ASN B 334 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 GLN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091329 restraints weight = 17775.530| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 3.17 r_work: 0.3121 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.9731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11362 Z= 0.152 Angle : 0.765 10.172 15516 Z= 0.369 Chirality : 0.044 0.212 1738 Planarity : 0.006 0.070 1980 Dihedral : 8.792 149.491 1568 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.90 % Allowed : 28.31 % Favored : 67.80 % 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: -0.23 (0.23), residues: 1382 helix: 2.49 (0.22), residues: 480 sheet: -0.42 (0.36), residues: 188 loop : -2.09 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 201 TYR 0.018 0.002 TYR E 626 PHE 0.025 0.002 PHE D 6 TRP 0.011 0.001 TRP E 678 HIS 0.006 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00357 (11362) covalent geometry : angle 0.76533 (15516) hydrogen bonds : bond 0.04880 ( 496) hydrogen bonds : angle 4.29741 ( 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 280 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.448 Fit side-chains REVERT: A 72 SER cc_start: 0.8620 (t) cc_final: 0.8374 (m) REVERT: A 349 LEU cc_start: 0.9172 (tt) cc_final: 0.8933 (tm) REVERT: A 352 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 131 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7020 (pp) REVERT: B 151 GLN cc_start: 0.8280 (tt0) cc_final: 0.7957 (tt0) REVERT: B 174 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7656 (t-90) REVERT: B 200 LEU cc_start: 0.8913 (tp) cc_final: 0.8675 (tp) REVERT: B 205 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8451 (ttp80) REVERT: B 251 GLU cc_start: 0.8577 (tt0) cc_final: 0.8033 (pt0) REVERT: B 312 PHE cc_start: 0.8891 (m-80) cc_final: 0.8602 (m-80) REVERT: B 313 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8506 (m) REVERT: B 446 ILE cc_start: 0.8800 (mt) cc_final: 0.8581 (mm) REVERT: B 525 LEU cc_start: 0.8324 (tp) cc_final: 0.7975 (tt) REVERT: B 560 ARG cc_start: 0.7587 (tmm-80) cc_final: 0.7343 (ttp80) REVERT: B 564 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8652 (t) REVERT: B 626 TYR cc_start: 0.8124 (m-80) cc_final: 0.7818 (m-80) REVERT: B 725 MET cc_start: 0.8461 (mpt) cc_final: 0.8246 (mpt) REVERT: D 1 MET cc_start: 0.6205 (tpp) cc_final: 0.5646 (mmt) REVERT: D 129 LYS cc_start: 0.8670 (tppt) cc_final: 0.8378 (ttpp) REVERT: D 349 LEU cc_start: 0.9129 (tt) cc_final: 0.8845 (tm) REVERT: D 354 GLU cc_start: 0.7862 (tp30) cc_final: 0.7648 (tp30) REVERT: E 131 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7382 (pp) REVERT: E 200 LEU cc_start: 0.9000 (tp) cc_final: 0.8711 (tp) REVERT: E 251 GLU cc_start: 0.8576 (tt0) cc_final: 0.8043 (pt0) REVERT: E 377 ASP cc_start: 0.8330 (t0) cc_final: 0.7993 (t70) REVERT: E 394 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8553 (m) REVERT: E 407 ASP cc_start: 0.8825 (t0) cc_final: 0.8608 (m-30) REVERT: E 623 SER cc_start: 0.9120 (t) cc_final: 0.8721 (p) REVERT: E 626 TYR cc_start: 0.7927 (m-80) cc_final: 0.7377 (m-80) outliers start: 46 outliers final: 14 residues processed: 260 average time/residue: 0.4657 time to fit residues: 132.9543 Evaluate side-chains 220 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 174 HIS Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 564 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 D residue 177 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 136 optimal weight: 0.0670 chunk 104 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** 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 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.110574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088406 restraints weight = 17720.765| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.14 r_work: 0.3057 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 1.0299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11362 Z= 0.193 Angle : 0.762 9.458 15516 Z= 0.373 Chirality : 0.045 0.195 1738 Planarity : 0.007 0.072 1980 Dihedral : 8.493 147.728 1568 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 5.08 % Allowed : 27.63 % 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: -0.07 (0.23), residues: 1382 helix: 2.63 (0.23), residues: 480 sheet: -0.85 (0.32), residues: 230 loop : -1.87 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 560 TYR 0.025 0.002 TYR E 382 PHE 0.015 0.002 PHE E 312 TRP 0.010 0.001 TRP B 169 HIS 0.008 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00464 (11362) covalent geometry : angle 0.76197 (15516) hydrogen bonds : bond 0.05400 ( 496) hydrogen bonds : angle 4.18517 ( 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 261 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 0.444 Fit side-chains REVERT: A 139 GLU cc_start: 0.8864 (tt0) cc_final: 0.8631 (tt0) REVERT: A 349 LEU cc_start: 0.9263 (tt) cc_final: 0.8990 (tm) REVERT: A 352 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 131 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7085 (pp) REVERT: B 151 GLN cc_start: 0.8264 (tt0) cc_final: 0.7841 (tt0) REVERT: B 174 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7729 (t-90) REVERT: B 200 LEU cc_start: 0.9028 (tp) cc_final: 0.8818 (tp) REVERT: B 205 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8594 (ttp80) REVERT: B 251 GLU cc_start: 0.8546 (tt0) cc_final: 0.8039 (pt0) REVERT: B 309 GLN cc_start: 0.8740 (tt0) cc_final: 0.8442 (tt0) REVERT: B 312 PHE cc_start: 0.9031 (m-80) cc_final: 0.8764 (m-80) REVERT: B 313 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8563 (m) REVERT: B 407 ASP cc_start: 0.8884 (t0) cc_final: 0.8643 (m-30) REVERT: B 446 ILE cc_start: 0.8799 (mt) cc_final: 0.8550 (mm) REVERT: B 525 LEU cc_start: 0.8430 (tp) cc_final: 0.8079 (tt) REVERT: B 560 ARG cc_start: 0.7698 (tmm-80) cc_final: 0.7416 (ttp80) REVERT: B 626 TYR cc_start: 0.7947 (m-80) cc_final: 0.7702 (m-80) REVERT: B 644 ASN cc_start: 0.7506 (m-40) cc_final: 0.7050 (p0) REVERT: D 1 MET cc_start: 0.6537 (tpp) cc_final: 0.5644 (mmt) REVERT: D 84 GLU cc_start: 0.8143 (tt0) cc_final: 0.7913 (pt0) REVERT: D 129 LYS cc_start: 0.8695 (tppt) cc_final: 0.8449 (ttpm) REVERT: D 349 LEU cc_start: 0.9249 (tt) cc_final: 0.8985 (tm) REVERT: D 354 GLU cc_start: 0.8069 (tp30) cc_final: 0.7779 (tp30) REVERT: E 131 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7264 (pp) REVERT: E 200 LEU cc_start: 0.9092 (tp) cc_final: 0.8808 (tp) REVERT: E 251 GLU cc_start: 0.8535 (tt0) cc_final: 0.8036 (pt0) REVERT: E 309 GLN cc_start: 0.8723 (tt0) cc_final: 0.8480 (tt0) REVERT: E 313 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8473 (m) REVERT: E 394 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8584 (m) REVERT: E 485 LEU cc_start: 0.8754 (tt) cc_final: 0.8441 (tp) outliers start: 60 outliers final: 28 residues processed: 241 average time/residue: 0.4944 time to fit residues: 129.8455 Evaluate side-chains 231 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR 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 177 VAL 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 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 205 ARG Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 505 LEU 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 177 VAL 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 242 HIS Chi-restraints excluded: chain E residue 313 SER 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 505 LEU Chi-restraints excluded: chain E residue 684 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 103 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 0.0050 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 11 optimal weight: 0.0050 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.113233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091385 restraints weight = 17328.840| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.10 r_work: 0.3112 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 1.0480 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= 0.126 Angle : 0.711 9.860 15516 Z= 0.344 Chirality : 0.042 0.162 1738 Planarity : 0.006 0.073 1980 Dihedral : 8.294 146.897 1568 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.24 % Allowed : 28.64 % Favored : 67.12 % 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: 0.25 (0.24), residues: 1382 helix: 2.90 (0.23), residues: 480 sheet: -0.29 (0.36), residues: 188 loop : -1.77 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 560 TYR 0.024 0.001 TYR E 382 PHE 0.029 0.001 PHE E 312 TRP 0.010 0.001 TRP B 400 HIS 0.005 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00286 (11362) covalent geometry : angle 0.71102 (15516) hydrogen bonds : bond 0.04327 ( 496) hydrogen bonds : angle 3.98967 ( 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 252 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.325 Fit side-chains REVERT: A 139 GLU cc_start: 0.8900 (tt0) cc_final: 0.8671 (tt0) REVERT: A 141 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8103 (tmm-80) REVERT: A 349 LEU cc_start: 0.9293 (tt) cc_final: 0.9063 (tm) REVERT: B 151 GLN cc_start: 0.8308 (tt0) cc_final: 0.7996 (tt0) REVERT: B 174 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7688 (t-90) REVERT: B 200 LEU cc_start: 0.9040 (tp) cc_final: 0.8818 (tp) REVERT: B 205 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8580 (ttp80) REVERT: B 251 GLU cc_start: 0.8548 (tt0) cc_final: 0.8096 (pt0) REVERT: B 312 PHE cc_start: 0.8957 (m-80) cc_final: 0.8726 (m-80) REVERT: B 313 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8535 (m) REVERT: B 407 ASP cc_start: 0.8872 (t0) cc_final: 0.8672 (m-30) REVERT: B 430 GLU cc_start: 0.8275 (tp30) cc_final: 0.7918 (tp30) REVERT: B 446 ILE cc_start: 0.8722 (mt) cc_final: 0.8452 (mm) REVERT: B 525 LEU cc_start: 0.8450 (tp) cc_final: 0.8109 (tt) REVERT: B 560 ARG cc_start: 0.7963 (tmm-80) cc_final: 0.7563 (ttp80) REVERT: B 623 SER cc_start: 0.9080 (t) cc_final: 0.8824 (t) REVERT: B 644 ASN cc_start: 0.7506 (m-40) cc_final: 0.7003 (p0) REVERT: D 1 MET cc_start: 0.6692 (tpp) cc_final: 0.5934 (mmt) REVERT: D 129 LYS cc_start: 0.8764 (tppt) cc_final: 0.8564 (ttpm) REVERT: D 352 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8283 (mt-10) REVERT: E 131 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7294 (pp) REVERT: E 200 LEU cc_start: 0.9105 (tp) cc_final: 0.8789 (tp) REVERT: E 251 GLU cc_start: 0.8530 (tt0) cc_final: 0.8051 (pt0) REVERT: E 309 GLN cc_start: 0.8665 (tt0) cc_final: 0.8442 (tt0) REVERT: E 313 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8381 (m) REVERT: E 394 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8544 (m) REVERT: E 485 LEU cc_start: 0.8670 (tt) cc_final: 0.8372 (tp) REVERT: E 687 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8244 (ttmm) outliers start: 50 outliers final: 17 residues processed: 234 average time/residue: 0.5234 time to fit residues: 132.8962 Evaluate side-chains 216 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 362 ILE 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 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 351 MET 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 687 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 334 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B 689 ASN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088014 restraints weight = 17559.121| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.10 r_work: 0.3059 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 1.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11362 Z= 0.185 Angle : 0.735 9.567 15516 Z= 0.356 Chirality : 0.044 0.160 1738 Planarity : 0.006 0.070 1980 Dihedral : 8.275 146.145 1568 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.07 % Allowed : 28.81 % Favored : 67.12 % 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: 0.20 (0.24), residues: 1382 helix: 2.72 (0.23), residues: 492 sheet: -0.26 (0.37), residues: 190 loop : -1.79 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 560 TYR 0.023 0.002 TYR B 382 PHE 0.029 0.002 PHE E 312 TRP 0.010 0.001 TRP B 400 HIS 0.005 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00448 (11362) covalent geometry : angle 0.73494 (15516) hydrogen bonds : bond 0.05207 ( 496) hydrogen bonds : angle 4.09032 ( 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 235 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7598 (t-90) REVERT: B 251 GLU cc_start: 0.8538 (tt0) cc_final: 0.8308 (tt0) REVERT: B 309 GLN cc_start: 0.8698 (tt0) cc_final: 0.8234 (mt0) REVERT: B 312 PHE cc_start: 0.8981 (m-80) cc_final: 0.8751 (m-80) REVERT: B 313 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8550 (m) REVERT: B 438 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 525 LEU cc_start: 0.8498 (tp) cc_final: 0.8135 (tt) REVERT: B 557 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6990 (pp20) REVERT: B 560 ARG cc_start: 0.8063 (tmm-80) cc_final: 0.7626 (ttp80) REVERT: B 623 SER cc_start: 0.9084 (t) cc_final: 0.8835 (t) REVERT: B 644 ASN cc_start: 0.7573 (m-40) cc_final: 0.7184 (p0) REVERT: D 129 LYS cc_start: 0.8828 (tppt) cc_final: 0.8608 (ttpm) REVERT: D 352 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8350 (mt-10) REVERT: E 131 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7383 (pp) REVERT: E 174 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7765 (t-90) REVERT: E 200 LEU cc_start: 0.9152 (tp) cc_final: 0.8918 (tp) REVERT: E 251 GLU cc_start: 0.8501 (tt0) cc_final: 0.8094 (pt0) REVERT: E 309 GLN cc_start: 0.8700 (tt0) cc_final: 0.8245 (mt0) REVERT: E 313 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8378 (m) REVERT: E 394 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8559 (m) REVERT: E 407 ASP cc_start: 0.8950 (m-30) cc_final: 0.8640 (m-30) REVERT: E 644 ASN cc_start: 0.7636 (m-40) cc_final: 0.7106 (m110) outliers start: 48 outliers final: 24 residues processed: 215 average time/residue: 0.5025 time to fit residues: 117.7515 Evaluate side-chains 210 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR 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 177 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 362 ILE 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 189 ILE Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 557 GLU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 94 TYR Chi-restraints excluded: chain D residue 122 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 174 HIS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 338 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 HIS B 480 GLN B 689 ASN ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090158 restraints weight = 17247.777| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.08 r_work: 0.3091 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 1.0925 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= 0.132 Angle : 0.714 11.583 15516 Z= 0.342 Chirality : 0.042 0.154 1738 Planarity : 0.006 0.066 1980 Dihedral : 8.115 144.979 1568 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.39 % Allowed : 29.66 % Favored : 66.95 % 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 (0.24), residues: 1382 helix: 2.92 (0.23), residues: 480 sheet: -0.24 (0.37), residues: 190 loop : -1.70 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 560 TYR 0.016 0.001 TYR B 626 PHE 0.030 0.001 PHE E 312 TRP 0.010 0.001 TRP D 168 HIS 0.006 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00305 (11362) covalent geometry : angle 0.71361 (15516) hydrogen bonds : bond 0.04383 ( 496) hydrogen bonds : angle 3.97447 ( 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 223 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8091 (tmm-80) REVERT: A 362 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8949 (pt) REVERT: B 165 ASP cc_start: 0.8011 (t0) cc_final: 0.7758 (m-30) REVERT: B 174 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7604 (t-90) REVERT: B 251 GLU cc_start: 0.8523 (tt0) cc_final: 0.7824 (tm-30) REVERT: B 309 GLN cc_start: 0.8683 (tt0) cc_final: 0.8225 (mt0) REVERT: B 312 PHE cc_start: 0.8935 (m-80) cc_final: 0.8729 (m-80) REVERT: B 313 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8522 (m) REVERT: B 446 ILE cc_start: 0.8751 (mt) cc_final: 0.8505 (mm) REVERT: B 525 LEU cc_start: 0.8520 (tp) cc_final: 0.8167 (tt) REVERT: B 557 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7141 (pp20) REVERT: B 560 ARG cc_start: 0.8074 (tmm-80) cc_final: 0.7652 (ttp80) REVERT: B 623 SER cc_start: 0.9049 (t) cc_final: 0.8762 (t) REVERT: B 644 ASN cc_start: 0.7580 (m-40) cc_final: 0.7178 (p0) REVERT: D 23 TYR cc_start: 0.8729 (m-80) cc_final: 0.8212 (m-80) REVERT: D 129 LYS cc_start: 0.8813 (tppt) cc_final: 0.8612 (ttpm) REVERT: D 352 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8268 (mt-10) REVERT: D 362 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8957 (pt) REVERT: E 131 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7323 (pp) REVERT: E 174 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7718 (t-90) REVERT: E 200 LEU cc_start: 0.9160 (tp) cc_final: 0.8909 (tp) REVERT: E 251 GLU cc_start: 0.8502 (tt0) cc_final: 0.8123 (pt0) REVERT: E 309 GLN cc_start: 0.8691 (tt0) cc_final: 0.8250 (mt0) REVERT: E 313 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8350 (m) REVERT: E 394 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8588 (m) REVERT: E 407 ASP cc_start: 0.8952 (m-30) cc_final: 0.8641 (m-30) REVERT: E 644 ASN cc_start: 0.7667 (m-40) cc_final: 0.7164 (m110) outliers start: 40 outliers final: 13 residues processed: 208 average time/residue: 0.5110 time to fit residues: 115.5620 Evaluate side-chains 193 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 362 ILE 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 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 122 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 174 HIS 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 338 SER Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 130 optimal weight: 0.0470 chunk 55 optimal weight: 2.9990 chunk 124 optimal weight: 0.0670 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS ** B 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 480 GLN ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092089 restraints weight = 17576.690| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.11 r_work: 0.3099 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 1.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11362 Z= 0.121 Angle : 0.712 12.093 15516 Z= 0.338 Chirality : 0.042 0.148 1738 Planarity : 0.006 0.062 1980 Dihedral : 7.911 143.058 1568 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.95 % Allowed : 31.61 % 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: 0.41 (0.24), residues: 1382 helix: 3.05 (0.23), residues: 480 sheet: -0.30 (0.35), residues: 204 loop : -1.68 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 560 TYR 0.023 0.001 TYR E 382 PHE 0.027 0.001 PHE E 312 TRP 0.012 0.001 TRP D 168 HIS 0.010 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00275 (11362) covalent geometry : angle 0.71248 (15516) hydrogen bonds : bond 0.03740 ( 496) hydrogen bonds : angle 3.88084 ( 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 210 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 174 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7569 (t-90) REVERT: B 205 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8443 (ttp80) REVERT: B 206 LEU cc_start: 0.8896 (mp) cc_final: 0.8658 (mt) REVERT: B 251 GLU cc_start: 0.8513 (tt0) cc_final: 0.8174 (pt0) REVERT: B 309 GLN cc_start: 0.8667 (tt0) cc_final: 0.8236 (mt0) REVERT: B 312 PHE cc_start: 0.8896 (m-80) cc_final: 0.8671 (m-80) REVERT: B 313 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8530 (m) REVERT: B 525 LEU cc_start: 0.8524 (tp) cc_final: 0.8176 (tt) REVERT: B 560 ARG cc_start: 0.8163 (tmm-80) cc_final: 0.7807 (ttp80) REVERT: B 623 SER cc_start: 0.8986 (t) cc_final: 0.8720 (t) REVERT: B 644 ASN cc_start: 0.7575 (m-40) cc_final: 0.7125 (p0) REVERT: D 23 TYR cc_start: 0.8701 (m-80) cc_final: 0.8258 (m-80) REVERT: E 131 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7195 (pp) REVERT: E 174 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7658 (t-90) REVERT: E 200 LEU cc_start: 0.9171 (tp) cc_final: 0.8893 (tp) REVERT: E 202 GLU cc_start: 0.8742 (tt0) cc_final: 0.8401 (tp30) REVERT: E 251 GLU cc_start: 0.8505 (tt0) cc_final: 0.8175 (pt0) REVERT: E 309 GLN cc_start: 0.8626 (tt0) cc_final: 0.8216 (mt0) REVERT: E 313 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8172 (m) REVERT: E 407 ASP cc_start: 0.8947 (m-30) cc_final: 0.8655 (m-30) REVERT: E 644 ASN cc_start: 0.7688 (m-40) cc_final: 0.7212 (m-40) outliers start: 23 outliers final: 10 residues processed: 200 average time/residue: 0.4874 time to fit residues: 106.3820 Evaluate side-chains 192 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 177 VAL 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 449 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain E residue 187 THR Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 0.3980 chunk 55 optimal weight: 0.0000 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 107 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 480 GLN D 146 HIS ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 689 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.114675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.092889 restraints weight = 17428.252| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.13 r_work: 0.3137 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 1.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11362 Z= 0.120 Angle : 0.715 12.260 15516 Z= 0.340 Chirality : 0.041 0.145 1738 Planarity : 0.006 0.057 1980 Dihedral : 7.757 141.752 1568 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.95 % Allowed : 31.69 % 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: 0.43 (0.24), residues: 1382 helix: 3.09 (0.23), residues: 480 sheet: -0.28 (0.36), residues: 204 loop : -1.68 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 560 TYR 0.028 0.001 TYR E 382 PHE 0.033 0.001 PHE E 312 TRP 0.011 0.001 TRP A 168 HIS 0.010 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00270 (11362) covalent geometry : angle 0.71545 (15516) hydrogen bonds : bond 0.03488 ( 496) hydrogen bonds : angle 3.80077 ( 1470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.97 seconds wall clock time: 57 minutes 58.53 seconds (3478.53 seconds total)