Starting phenix.real_space_refine on Tue Mar 11 19:34:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gau_29908/03_2025/8gau_29908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gau_29908/03_2025/8gau_29908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gau_29908/03_2025/8gau_29908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gau_29908/03_2025/8gau_29908.map" model { file = "/net/cci-nas-00/data/ceres_data/8gau_29908/03_2025/8gau_29908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gau_29908/03_2025/8gau_29908.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.035 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4163 2.51 5 N 1133 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6604 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2987 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "M" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "N" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.53, per 1000 atoms: 0.69 Number of scatterers: 6604 At special positions: 0 Unit cell: (105.45, 93.24, 113.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1274 8.00 N 1133 7.00 C 4163 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.00 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 200 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 987.5 milliseconds 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 20 sheets defined 2.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.674A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'H' and resid 99 through 100C removed outlier: 3.757A pdb=" N VAL H 100B" --> pdb=" O TYR H 99 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS H 100C" --> pdb=" O ASP H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 99 through 100C' Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.717A pdb=" N ASP M 31 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.715A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 6.828A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 121 removed outlier: 5.372A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 133 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.659A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 203 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.969A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS A 264 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.715A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.834A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 356 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 362 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 377 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU A 372 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLU A 399 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.542A pdb=" N SER H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.505A pdb=" N GLU H 50 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.827A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 34 through 37 removed outlier: 3.802A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 62 through 63 Processing sheet with id=AB4, first strand: chain 'L' and resid 66 through 67 removed outlier: 3.853A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.762A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 18 through 21 removed outlier: 3.645A pdb=" N LEU M 18 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE M 82 " --> pdb=" O LEU M 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER M 70 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.890A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.890A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.592A pdb=" N SER N 63 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.599A pdb=" N ASP N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.694A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN N 38 " --> pdb=" O THR N 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1971 1.33 - 1.46: 1709 1.46 - 1.58: 3047 1.58 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 6769 Sorted by residual: bond pdb=" N CYS A 183 " pdb=" CA CYS A 183 " ideal model delta sigma weight residual 1.455 1.494 -0.040 1.32e-02 5.74e+03 8.98e+00 bond pdb=" N HIS A 184 " pdb=" CA HIS A 184 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.49e+00 bond pdb=" N ARG A 327 " pdb=" CA ARG A 327 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.16e-02 7.43e+03 7.40e+00 bond pdb=" N ASN A 367 " pdb=" CA ASN A 367 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.28e+00 bond pdb=" N ASP A 359 " pdb=" CA ASP A 359 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.36e-02 5.41e+03 6.93e+00 ... (remaining 6764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8703 2.13 - 4.27: 418 4.27 - 6.40: 59 6.40 - 8.53: 14 8.53 - 10.67: 3 Bond angle restraints: 9197 Sorted by residual: angle pdb=" CA PHE H 31 " pdb=" C PHE H 31 " pdb=" O PHE H 31 " ideal model delta sigma weight residual 120.43 113.36 7.07 1.12e+00 7.97e-01 3.99e+01 angle pdb=" N ARG H 66 " pdb=" CA ARG H 66 " pdb=" C ARG H 66 " ideal model delta sigma weight residual 114.39 105.95 8.44 1.45e+00 4.76e-01 3.39e+01 angle pdb=" C PRO A 326 " pdb=" CA PRO A 326 " pdb=" CB PRO A 326 " ideal model delta sigma weight residual 111.40 116.04 -4.64 9.10e-01 1.21e+00 2.60e+01 angle pdb=" CA ARG A 430 " pdb=" C ARG A 430 " pdb=" O ARG A 430 " ideal model delta sigma weight residual 122.01 116.67 5.34 1.05e+00 9.07e-01 2.58e+01 angle pdb=" C VAL H 100B" pdb=" N HIS H 100C" pdb=" CA HIS H 100C" ideal model delta sigma weight residual 120.54 127.19 -6.65 1.35e+00 5.49e-01 2.42e+01 ... (remaining 9192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 3746 14.99 - 29.99: 170 29.99 - 44.98: 58 44.98 - 59.97: 16 59.97 - 74.96: 5 Dihedral angle restraints: 3995 sinusoidal: 1579 harmonic: 2416 Sorted by residual: dihedral pdb=" CA ARG M 13 " pdb=" C ARG M 13 " pdb=" N PRO M 14 " pdb=" CA PRO M 14 " ideal model delta harmonic sigma weight residual -180.00 -145.43 -34.57 0 5.00e+00 4.00e-02 4.78e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 152.36 -59.36 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CD ARG A 430 " pdb=" NE ARG A 430 " pdb=" CZ ARG A 430 " pdb=" NH1 ARG A 430 " ideal model delta sinusoidal sigma weight residual 0.00 -58.81 58.81 1 1.00e+01 1.00e-02 4.63e+01 ... (remaining 3992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 752 0.064 - 0.129: 200 0.129 - 0.193: 42 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 997 Sorted by residual: chirality pdb=" CA PHE H 33 " pdb=" N PHE H 33 " pdb=" C PHE H 33 " pdb=" CB PHE H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB ILE H 60 " pdb=" CA ILE H 60 " pdb=" CG1 ILE H 60 " pdb=" CG2 ILE H 60 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PHE H 31 " pdb=" N PHE H 31 " pdb=" C PHE H 31 " pdb=" CB PHE H 31 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 994 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 430 " -0.933 9.50e-02 1.11e+02 4.18e-01 1.06e+02 pdb=" NE ARG A 430 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 430 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 430 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 430 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 327 " -0.321 9.50e-02 1.11e+02 1.44e-01 1.27e+01 pdb=" NE ARG A 327 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 327 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 327 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 327 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 28 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C SER H 28 " 0.051 2.00e-02 2.50e+03 pdb=" O SER H 28 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE H 29 " -0.017 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1820 2.81 - 3.33: 5138 3.33 - 3.85: 10435 3.85 - 4.38: 11342 4.38 - 4.90: 20836 Nonbonded interactions: 49571 Sorted by model distance: nonbonded pdb=" OG SER A 217 " pdb=" OD2 ASP A 243 " model vdw 2.285 3.040 nonbonded pdb=" OE1 GLN A 136 " pdb=" NH1 ARG A 156 " model vdw 2.303 3.120 nonbonded pdb=" OE2 GLU A 277 " pdb=" OH TYR M 100A" model vdw 2.310 3.040 nonbonded pdb=" OG SER M 17 " pdb=" OD1 ASN M 82A" model vdw 2.353 3.040 nonbonded pdb=" OH TYR H 32 " pdb=" O PRO H 100H" model vdw 2.365 3.040 ... (remaining 49566 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 0.050 6769 Z= 0.405 Angle : 1.044 10.666 9197 Z= 0.606 Chirality : 0.061 0.322 997 Planarity : 0.015 0.418 1179 Dihedral : 10.366 74.963 2426 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.11 % Favored : 89.54 % Rotamer: Outliers : 0.96 % Allowed : 3.17 % Favored : 95.87 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.24), residues: 841 helix: -4.72 (0.38), residues: 6 sheet: -2.42 (0.25), residues: 346 loop : -3.37 (0.22), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP M 103 HIS 0.004 0.001 HIS A 264 PHE 0.028 0.003 PHE H 78 TYR 0.036 0.003 TYR M 32 ARG 0.010 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 301 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8254 (mttt) cc_final: 0.7832 (mmtt) REVERT: A 104 ASN cc_start: 0.8403 (m-40) cc_final: 0.8119 (m110) REVERT: A 105 SER cc_start: 0.8372 (t) cc_final: 0.8012 (m) REVERT: A 108 LEU cc_start: 0.8325 (mt) cc_final: 0.8122 (mt) REVERT: A 119 GLU cc_start: 0.7292 (mp0) cc_final: 0.6890 (mp0) REVERT: A 128 LYS cc_start: 0.8011 (pttm) cc_final: 0.7345 (pttm) REVERT: A 134 LEU cc_start: 0.8389 (mt) cc_final: 0.8108 (mp) REVERT: A 142 ASN cc_start: 0.8227 (t0) cc_final: 0.7856 (t0) REVERT: A 162 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 187 LYS cc_start: 0.8594 (mttt) cc_final: 0.8369 (mtmm) REVERT: A 206 ILE cc_start: 0.8664 (mt) cc_final: 0.8449 (mm) REVERT: A 229 GLU cc_start: 0.7510 (pt0) cc_final: 0.7302 (pt0) REVERT: A 233 ILE cc_start: 0.8602 (mt) cc_final: 0.8250 (mm) REVERT: A 236 THR cc_start: 0.8361 (m) cc_final: 0.8020 (p) REVERT: A 251 ASP cc_start: 0.7459 (m-30) cc_final: 0.7120 (m-30) REVERT: A 258 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6686 (mt-10) REVERT: A 265 ILE cc_start: 0.8888 (mt) cc_final: 0.8684 (mm) REVERT: A 302 ILE cc_start: 0.8671 (mt) cc_final: 0.8109 (mm) REVERT: A 307 VAL cc_start: 0.8665 (m) cc_final: 0.8398 (t) REVERT: A 309 ASN cc_start: 0.7478 (p0) cc_final: 0.7223 (t0) REVERT: A 319 SER cc_start: 0.8539 (t) cc_final: 0.8292 (p) REVERT: A 328 LYS cc_start: 0.8118 (mttt) cc_final: 0.7640 (mttt) REVERT: A 343 GLU cc_start: 0.7239 (mp0) cc_final: 0.6948 (mp0) REVERT: A 370 LEU cc_start: 0.8673 (mt) cc_final: 0.8470 (mm) REVERT: A 375 GLU cc_start: 0.7634 (pt0) cc_final: 0.7152 (pt0) REVERT: A 378 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7860 (ttpp) REVERT: A 380 ILE cc_start: 0.8127 (mt) cc_final: 0.7916 (mm) REVERT: A 385 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8064 (mtpp) REVERT: A 413 GLU cc_start: 0.7438 (tt0) cc_final: 0.7135 (tt0) REVERT: A 416 SER cc_start: 0.8892 (m) cc_final: 0.8404 (p) REVERT: A 427 ILE cc_start: 0.8161 (mt) cc_final: 0.7731 (tp) REVERT: A 433 GLU cc_start: 0.7590 (mp0) cc_final: 0.6787 (mp0) REVERT: A 437 TRP cc_start: 0.8286 (m100) cc_final: 0.7705 (m-10) REVERT: A 440 SER cc_start: 0.8643 (t) cc_final: 0.8296 (p) REVERT: A 445 VAL cc_start: 0.8368 (t) cc_final: 0.8029 (p) REVERT: H 13 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7362 (mtmm) REVERT: H 16 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7438 (mt-10) REVERT: H 22 CYS cc_start: 0.6132 (t) cc_final: 0.5752 (t) REVERT: H 29 PHE cc_start: 0.7984 (t80) cc_final: 0.7627 (t80) REVERT: H 31 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7291 (p90) REVERT: H 60 ILE cc_start: 0.8172 (tp) cc_final: 0.7957 (tp) REVERT: H 100 HIS cc_start: 0.7566 (t-90) cc_final: 0.7196 (t-90) REVERT: H 100 LEU cc_start: 0.8159 (mt) cc_final: 0.7783 (mt) REVERT: L 7 SER cc_start: 0.8699 (m) cc_final: 0.8351 (p) REVERT: L 58 VAL cc_start: 0.8839 (t) cc_final: 0.8540 (p) REVERT: L 103 LYS cc_start: 0.8068 (tttt) cc_final: 0.7431 (tttt) REVERT: L 104 VAL cc_start: 0.8152 (t) cc_final: 0.7911 (m) REVERT: M 32 TYR cc_start: 0.7842 (m-10) cc_final: 0.7384 (m-10) REVERT: N 26 SER cc_start: 0.8338 (p) cc_final: 0.8058 (m) REVERT: N 82 ASP cc_start: 0.8080 (m-30) cc_final: 0.7804 (m-30) REVERT: N 86 TYR cc_start: 0.8093 (m-10) cc_final: 0.7562 (m-80) REVERT: N 89 GLN cc_start: 0.7883 (tm130) cc_final: 0.7528 (tm130) REVERT: N 103 LYS cc_start: 0.7924 (tptt) cc_final: 0.7648 (tptt) outliers start: 7 outliers final: 3 residues processed: 303 average time/residue: 0.1900 time to fit residues: 74.7347 Evaluate side-chains 283 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 31 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 93 ASN A 147 ASN A 273 GLN A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 105 GLN L 55 GLN L 89 GLN M 81 HIS N 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093705 restraints weight = 11687.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096933 restraints weight = 4915.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.098936 restraints weight = 2510.999| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6769 Z= 0.190 Angle : 0.645 8.266 9197 Z= 0.338 Chirality : 0.047 0.156 997 Planarity : 0.006 0.052 1179 Dihedral : 6.403 58.873 959 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.44 % Allowed : 11.98 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.26), residues: 841 helix: -4.23 (0.54), residues: 6 sheet: -1.60 (0.29), residues: 323 loop : -2.97 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 7 HIS 0.002 0.001 HIS H 100C PHE 0.012 0.002 PHE H 78 TYR 0.020 0.002 TYR M 100A ARG 0.004 0.001 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8261 (mttt) cc_final: 0.7876 (mmtt) REVERT: A 104 ASN cc_start: 0.8331 (m-40) cc_final: 0.7989 (m110) REVERT: A 128 LYS cc_start: 0.7970 (pttm) cc_final: 0.7301 (pttm) REVERT: A 142 ASN cc_start: 0.8030 (t0) cc_final: 0.7770 (t0) REVERT: A 162 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 245 SER cc_start: 0.8491 (t) cc_final: 0.7930 (p) REVERT: A 249 LYS cc_start: 0.8401 (mttt) cc_final: 0.7516 (mtpp) REVERT: A 251 ASP cc_start: 0.7481 (m-30) cc_final: 0.7114 (m-30) REVERT: A 261 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7556 (tmmm) REVERT: A 276 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6648 (mm-30) REVERT: A 292 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7273 (ptt180) REVERT: A 302 ILE cc_start: 0.8570 (mt) cc_final: 0.8091 (mm) REVERT: A 309 ASN cc_start: 0.7444 (p0) cc_final: 0.7218 (t0) REVERT: A 327 ARG cc_start: 0.8290 (ptt-90) cc_final: 0.8073 (ptt-90) REVERT: A 343 GLU cc_start: 0.7399 (mp0) cc_final: 0.6856 (mp0) REVERT: A 356 ASP cc_start: 0.8230 (t0) cc_final: 0.8015 (t0) REVERT: A 370 LEU cc_start: 0.8699 (mt) cc_final: 0.8480 (mm) REVERT: A 375 GLU cc_start: 0.7673 (pt0) cc_final: 0.7097 (pt0) REVERT: A 378 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7905 (ttpt) REVERT: A 381 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7058 (mm-30) REVERT: A 385 LYS cc_start: 0.8366 (mmmt) cc_final: 0.8030 (mtpp) REVERT: A 388 SER cc_start: 0.8425 (t) cc_final: 0.7996 (p) REVERT: A 399 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6716 (mt-10) REVERT: A 413 GLU cc_start: 0.7332 (tt0) cc_final: 0.7100 (tt0) REVERT: A 416 SER cc_start: 0.8906 (m) cc_final: 0.8399 (p) REVERT: A 427 ILE cc_start: 0.8173 (mt) cc_final: 0.7760 (tp) REVERT: A 433 GLU cc_start: 0.7661 (mp0) cc_final: 0.7008 (mp0) REVERT: A 437 TRP cc_start: 0.8345 (m100) cc_final: 0.7576 (m-10) REVERT: A 453 TYR cc_start: 0.7864 (p90) cc_final: 0.7658 (p90) REVERT: A 463 ASP cc_start: 0.8010 (t0) cc_final: 0.7788 (t0) REVERT: H 7 TRP cc_start: 0.7562 (p-90) cc_final: 0.7343 (p-90) REVERT: H 13 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7431 (mtmm) REVERT: H 25 TYR cc_start: 0.7920 (m-80) cc_final: 0.7701 (m-10) REVERT: H 31 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6829 (p90) REVERT: H 100 HIS cc_start: 0.7407 (t-90) cc_final: 0.6958 (t-90) REVERT: H 100 LEU cc_start: 0.8060 (mt) cc_final: 0.7363 (mt) REVERT: L 4 MET cc_start: 0.5604 (mpp) cc_final: 0.5378 (mpp) REVERT: L 7 SER cc_start: 0.8629 (m) cc_final: 0.8223 (p) REVERT: L 58 VAL cc_start: 0.8797 (t) cc_final: 0.8507 (p) REVERT: L 103 LYS cc_start: 0.7763 (tttt) cc_final: 0.7279 (tttt) REVERT: L 107 LYS cc_start: 0.7652 (pttp) cc_final: 0.7246 (tppt) REVERT: M 32 TYR cc_start: 0.7708 (m-80) cc_final: 0.7441 (m-10) REVERT: M 59 TYR cc_start: 0.8218 (m-10) cc_final: 0.7836 (m-80) REVERT: M 96 SER cc_start: 0.8365 (m) cc_final: 0.7989 (p) REVERT: N 56 SER cc_start: 0.8646 (t) cc_final: 0.8277 (p) REVERT: N 82 ASP cc_start: 0.8204 (m-30) cc_final: 0.7735 (m-30) REVERT: N 86 TYR cc_start: 0.8097 (m-10) cc_final: 0.7890 (m-80) outliers start: 25 outliers final: 12 residues processed: 265 average time/residue: 0.2131 time to fit residues: 73.8851 Evaluate side-chains 255 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.0030 chunk 26 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS M 73 ASN N 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.089772 restraints weight = 11845.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092965 restraints weight = 4926.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.094889 restraints weight = 2496.577| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6769 Z= 0.399 Angle : 0.744 8.511 9197 Z= 0.392 Chirality : 0.049 0.153 997 Planarity : 0.006 0.064 1179 Dihedral : 6.467 48.366 958 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 4.68 % Allowed : 15.01 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.26), residues: 841 helix: -3.78 (1.32), residues: 6 sheet: -1.56 (0.28), residues: 330 loop : -3.04 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 7 HIS 0.005 0.001 HIS A 264 PHE 0.028 0.002 PHE H 78 TYR 0.029 0.003 TYR N 49 ARG 0.006 0.001 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8358 (mttt) cc_final: 0.7966 (mmtt) REVERT: A 119 GLU cc_start: 0.7454 (mp0) cc_final: 0.7169 (mp0) REVERT: A 128 LYS cc_start: 0.8035 (pttm) cc_final: 0.7707 (pttm) REVERT: A 236 THR cc_start: 0.8506 (m) cc_final: 0.8145 (p) REVERT: A 245 SER cc_start: 0.8538 (t) cc_final: 0.8040 (p) REVERT: A 249 LYS cc_start: 0.8436 (mttt) cc_final: 0.7876 (mttt) REVERT: A 251 ASP cc_start: 0.7635 (m-30) cc_final: 0.7317 (m-30) REVERT: A 258 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 261 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7758 (tmmm) REVERT: A 276 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6754 (mm-30) REVERT: A 292 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7171 (ptt180) REVERT: A 302 ILE cc_start: 0.8738 (mt) cc_final: 0.8278 (mm) REVERT: A 307 VAL cc_start: 0.8744 (m) cc_final: 0.8498 (t) REVERT: A 313 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8096 (t) REVERT: A 343 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 356 ASP cc_start: 0.8349 (t0) cc_final: 0.8144 (t0) REVERT: A 370 LEU cc_start: 0.8799 (mt) cc_final: 0.8546 (mm) REVERT: A 375 GLU cc_start: 0.7643 (pt0) cc_final: 0.7105 (pt0) REVERT: A 378 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8059 (ttpt) REVERT: A 385 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8003 (mtpp) REVERT: A 388 SER cc_start: 0.8549 (t) cc_final: 0.7998 (p) REVERT: A 389 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8564 (mtpp) REVERT: A 413 GLU cc_start: 0.7350 (tt0) cc_final: 0.7048 (tt0) REVERT: A 416 SER cc_start: 0.8943 (m) cc_final: 0.8448 (p) REVERT: A 427 ILE cc_start: 0.8257 (mt) cc_final: 0.7814 (tt) REVERT: A 430 ARG cc_start: 0.8162 (tpt170) cc_final: 0.7871 (tpt170) REVERT: A 433 GLU cc_start: 0.7721 (mp0) cc_final: 0.7040 (mp0) REVERT: A 437 TRP cc_start: 0.8404 (m100) cc_final: 0.7334 (m-10) REVERT: A 440 SER cc_start: 0.8545 (t) cc_final: 0.8317 (t) REVERT: A 453 TYR cc_start: 0.8036 (p90) cc_final: 0.7733 (p90) REVERT: H 7 TRP cc_start: 0.7644 (p-90) cc_final: 0.7303 (p-90) REVERT: H 13 LYS cc_start: 0.7765 (mtmm) cc_final: 0.7407 (mtmm) REVERT: H 16 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7407 (mt-10) REVERT: H 21 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7942 (p) REVERT: H 81 LYS cc_start: 0.8177 (mttt) cc_final: 0.7882 (mptt) REVERT: H 99 TYR cc_start: 0.7916 (m-80) cc_final: 0.7456 (m-80) REVERT: H 100 LEU cc_start: 0.8274 (mt) cc_final: 0.7973 (mp) REVERT: L 7 SER cc_start: 0.8848 (m) cc_final: 0.8350 (p) REVERT: L 22 THR cc_start: 0.7819 (p) cc_final: 0.7468 (p) REVERT: L 24 ARG cc_start: 0.7204 (mmm160) cc_final: 0.6593 (tpm170) REVERT: L 45 LYS cc_start: 0.8334 (tttt) cc_final: 0.8130 (tttt) REVERT: L 58 VAL cc_start: 0.8837 (t) cc_final: 0.8536 (p) REVERT: L 103 LYS cc_start: 0.7874 (tttt) cc_final: 0.7341 (tttt) REVERT: M 32 TYR cc_start: 0.7933 (m-80) cc_final: 0.7549 (m-10) REVERT: N 24 ARG cc_start: 0.7232 (ttm170) cc_final: 0.7019 (ttm170) REVERT: N 56 SER cc_start: 0.8628 (t) cc_final: 0.8259 (p) REVERT: N 67 TYR cc_start: 0.8391 (t80) cc_final: 0.8090 (t80) REVERT: N 82 ASP cc_start: 0.8237 (m-30) cc_final: 0.7967 (m-30) REVERT: N 86 TYR cc_start: 0.8082 (m-10) cc_final: 0.7574 (m-80) outliers start: 34 outliers final: 23 residues processed: 271 average time/residue: 0.1990 time to fit residues: 69.5695 Evaluate side-chains 277 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 226 GLN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.091215 restraints weight = 11844.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.094431 restraints weight = 4953.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096399 restraints weight = 2513.685| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6769 Z= 0.245 Angle : 0.654 9.135 9197 Z= 0.342 Chirality : 0.047 0.165 997 Planarity : 0.005 0.056 1179 Dihedral : 5.959 47.116 958 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 5.10 % Allowed : 17.36 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.27), residues: 841 helix: -3.21 (1.82), residues: 6 sheet: -1.26 (0.29), residues: 329 loop : -2.82 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 7 HIS 0.008 0.001 HIS H 53 PHE 0.021 0.002 PHE H 78 TYR 0.030 0.002 TYR N 49 ARG 0.003 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8330 (mttt) cc_final: 0.7967 (mmtt) REVERT: A 128 LYS cc_start: 0.8065 (pttm) cc_final: 0.7846 (pttm) REVERT: A 245 SER cc_start: 0.8547 (t) cc_final: 0.8019 (p) REVERT: A 251 ASP cc_start: 0.7640 (m-30) cc_final: 0.7325 (m-30) REVERT: A 261 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8146 (tptm) REVERT: A 271 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 276 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6791 (mm-30) REVERT: A 292 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7382 (ptt180) REVERT: A 302 ILE cc_start: 0.8735 (mt) cc_final: 0.8242 (mm) REVERT: A 307 VAL cc_start: 0.8635 (m) cc_final: 0.8317 (t) REVERT: A 309 ASN cc_start: 0.7598 (t0) cc_final: 0.7225 (t0) REVERT: A 313 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8062 (t) REVERT: A 343 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6838 (mp0) REVERT: A 356 ASP cc_start: 0.8270 (t0) cc_final: 0.8018 (t0) REVERT: A 370 LEU cc_start: 0.8805 (mt) cc_final: 0.8555 (mm) REVERT: A 375 GLU cc_start: 0.7588 (pt0) cc_final: 0.7078 (pt0) REVERT: A 378 LYS cc_start: 0.8300 (ttpt) cc_final: 0.8079 (ttpt) REVERT: A 385 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8079 (mtpp) REVERT: A 388 SER cc_start: 0.8569 (t) cc_final: 0.8025 (p) REVERT: A 389 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8464 (mttp) REVERT: A 413 GLU cc_start: 0.7302 (tt0) cc_final: 0.7007 (tt0) REVERT: A 416 SER cc_start: 0.8948 (m) cc_final: 0.8435 (p) REVERT: A 427 ILE cc_start: 0.8171 (mt) cc_final: 0.7838 (tt) REVERT: A 430 ARG cc_start: 0.8126 (tpt170) cc_final: 0.7920 (tpt170) REVERT: A 433 GLU cc_start: 0.7822 (mp0) cc_final: 0.7249 (mp0) REVERT: A 437 TRP cc_start: 0.8374 (m100) cc_final: 0.7432 (m-10) REVERT: A 440 SER cc_start: 0.8510 (t) cc_final: 0.8240 (t) REVERT: A 453 TYR cc_start: 0.8063 (p90) cc_final: 0.7725 (p90) REVERT: H 7 TRP cc_start: 0.7519 (p-90) cc_final: 0.7185 (p-90) REVERT: H 13 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7402 (mtmm) REVERT: H 16 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7337 (mt-10) REVERT: H 81 LYS cc_start: 0.8159 (mttt) cc_final: 0.7858 (mptt) REVERT: H 99 TYR cc_start: 0.7888 (m-80) cc_final: 0.7416 (m-80) REVERT: H 100 LEU cc_start: 0.8175 (mt) cc_final: 0.7953 (mp) REVERT: L 7 SER cc_start: 0.8757 (m) cc_final: 0.8309 (p) REVERT: L 45 LYS cc_start: 0.8331 (tttt) cc_final: 0.8128 (tttt) REVERT: L 58 VAL cc_start: 0.8863 (t) cc_final: 0.8561 (p) REVERT: L 103 LYS cc_start: 0.7922 (tttt) cc_final: 0.7355 (tttt) REVERT: M 32 TYR cc_start: 0.7769 (m-80) cc_final: 0.7545 (m-10) REVERT: M 59 TYR cc_start: 0.8429 (m-80) cc_final: 0.8014 (m-80) REVERT: M 96 SER cc_start: 0.8277 (m) cc_final: 0.8064 (p) REVERT: N 56 SER cc_start: 0.8619 (t) cc_final: 0.8293 (p) REVERT: N 67 TYR cc_start: 0.8399 (t80) cc_final: 0.7906 (t80) REVERT: N 86 TYR cc_start: 0.8049 (m-10) cc_final: 0.7471 (m-80) outliers start: 37 outliers final: 25 residues processed: 263 average time/residue: 0.2042 time to fit residues: 68.9960 Evaluate side-chains 270 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 184 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS N 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.105007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.092731 restraints weight = 11737.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095896 restraints weight = 4903.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097853 restraints weight = 2483.855| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6769 Z= 0.225 Angle : 0.634 8.461 9197 Z= 0.328 Chirality : 0.047 0.168 997 Planarity : 0.005 0.053 1179 Dihedral : 5.727 47.526 958 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.37 % Allowed : 17.22 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.27), residues: 841 helix: -2.80 (2.17), residues: 6 sheet: -1.25 (0.28), residues: 354 loop : -2.75 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 7 HIS 0.006 0.001 HIS H 53 PHE 0.021 0.002 PHE H 78 TYR 0.023 0.002 TYR M 100A ARG 0.003 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8323 (mttt) cc_final: 0.7963 (mmtt) REVERT: A 128 LYS cc_start: 0.8089 (pttm) cc_final: 0.7828 (pttm) REVERT: A 245 SER cc_start: 0.8534 (t) cc_final: 0.8055 (p) REVERT: A 251 ASP cc_start: 0.7673 (m-30) cc_final: 0.7368 (m-30) REVERT: A 252 THR cc_start: 0.8623 (m) cc_final: 0.8362 (t) REVERT: A 261 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7791 (tmmm) REVERT: A 271 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8565 (p) REVERT: A 292 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7443 (ptt180) REVERT: A 302 ILE cc_start: 0.8729 (mt) cc_final: 0.8246 (mm) REVERT: A 306 ASN cc_start: 0.7871 (t0) cc_final: 0.7591 (t0) REVERT: A 307 VAL cc_start: 0.8610 (m) cc_final: 0.8183 (t) REVERT: A 309 ASN cc_start: 0.7623 (t0) cc_final: 0.7205 (t0) REVERT: A 316 TYR cc_start: 0.7968 (m-10) cc_final: 0.7608 (m-10) REVERT: A 343 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 356 ASP cc_start: 0.8211 (t0) cc_final: 0.7998 (t0) REVERT: A 370 LEU cc_start: 0.8754 (mt) cc_final: 0.8509 (mm) REVERT: A 375 GLU cc_start: 0.7585 (pt0) cc_final: 0.7059 (pt0) REVERT: A 378 LYS cc_start: 0.8301 (ttpt) cc_final: 0.8068 (ttpt) REVERT: A 385 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8098 (mtpp) REVERT: A 388 SER cc_start: 0.8607 (t) cc_final: 0.8068 (p) REVERT: A 389 LYS cc_start: 0.8956 (mtpp) cc_final: 0.8753 (mttm) REVERT: A 413 GLU cc_start: 0.7285 (tt0) cc_final: 0.7025 (tt0) REVERT: A 416 SER cc_start: 0.8950 (m) cc_final: 0.8446 (p) REVERT: A 427 ILE cc_start: 0.8137 (mt) cc_final: 0.7723 (tt) REVERT: A 430 ARG cc_start: 0.8130 (tpt170) cc_final: 0.7929 (tpt170) REVERT: A 433 GLU cc_start: 0.7805 (mp0) cc_final: 0.7165 (mp0) REVERT: A 437 TRP cc_start: 0.8356 (m100) cc_final: 0.7393 (m-10) REVERT: A 440 SER cc_start: 0.8484 (t) cc_final: 0.8220 (t) REVERT: A 453 TYR cc_start: 0.8088 (p90) cc_final: 0.7699 (p90) REVERT: H 7 TRP cc_start: 0.7515 (p-90) cc_final: 0.7228 (p-90) REVERT: H 13 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7388 (mtmm) REVERT: H 16 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7279 (mt-10) REVERT: H 81 LYS cc_start: 0.8141 (mttt) cc_final: 0.7867 (mptt) REVERT: H 99 TYR cc_start: 0.7907 (m-80) cc_final: 0.7410 (m-80) REVERT: H 100 LEU cc_start: 0.8092 (mt) cc_final: 0.7831 (mp) REVERT: L 7 SER cc_start: 0.8731 (m) cc_final: 0.8295 (p) REVERT: L 45 LYS cc_start: 0.8330 (tttt) cc_final: 0.8102 (tttt) REVERT: L 58 VAL cc_start: 0.8864 (t) cc_final: 0.8565 (p) REVERT: L 103 LYS cc_start: 0.7844 (tttt) cc_final: 0.7291 (tttt) REVERT: M 32 TYR cc_start: 0.7768 (m-80) cc_final: 0.7552 (m-10) REVERT: M 59 TYR cc_start: 0.8471 (m-80) cc_final: 0.7937 (m-80) REVERT: M 96 SER cc_start: 0.8276 (m) cc_final: 0.8041 (p) REVERT: N 24 ARG cc_start: 0.7113 (ttm170) cc_final: 0.6682 (ttm110) REVERT: N 56 SER cc_start: 0.8648 (t) cc_final: 0.8333 (p) REVERT: N 67 TYR cc_start: 0.8447 (t80) cc_final: 0.7862 (t80) REVERT: N 86 TYR cc_start: 0.8000 (m-10) cc_final: 0.7406 (m-80) outliers start: 39 outliers final: 28 residues processed: 259 average time/residue: 0.2152 time to fit residues: 72.4416 Evaluate side-chains 271 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 239 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 0.0060 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 309 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.094198 restraints weight = 11705.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097371 restraints weight = 4864.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099251 restraints weight = 2454.552| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6769 Z= 0.153 Angle : 0.603 8.270 9197 Z= 0.309 Chirality : 0.046 0.175 997 Planarity : 0.005 0.045 1179 Dihedral : 5.386 47.475 958 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.23 % Allowed : 18.46 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.27), residues: 841 helix: -2.81 (2.19), residues: 6 sheet: -0.94 (0.28), residues: 346 loop : -2.57 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 36 HIS 0.002 0.001 HIS A 184 PHE 0.017 0.001 PHE H 78 TYR 0.028 0.001 TYR N 49 ARG 0.005 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8288 (mttt) cc_final: 0.7897 (mmtt) REVERT: A 162 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 245 SER cc_start: 0.8452 (t) cc_final: 0.8117 (p) REVERT: A 249 LYS cc_start: 0.8422 (mttt) cc_final: 0.7519 (mtpp) REVERT: A 251 ASP cc_start: 0.7679 (m-30) cc_final: 0.7434 (m-30) REVERT: A 261 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7805 (tmmm) REVERT: A 271 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 292 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7115 (ptt180) REVERT: A 302 ILE cc_start: 0.8676 (mt) cc_final: 0.8187 (mm) REVERT: A 307 VAL cc_start: 0.8534 (m) cc_final: 0.8196 (t) REVERT: A 309 ASN cc_start: 0.7672 (t0) cc_final: 0.7093 (t0) REVERT: A 316 TYR cc_start: 0.7915 (m-10) cc_final: 0.7695 (m-10) REVERT: A 327 ARG cc_start: 0.8385 (ptt-90) cc_final: 0.8171 (ptt-90) REVERT: A 343 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: A 370 LEU cc_start: 0.8725 (mt) cc_final: 0.8506 (mm) REVERT: A 375 GLU cc_start: 0.7597 (pt0) cc_final: 0.7147 (pt0) REVERT: A 378 LYS cc_start: 0.8278 (ttpt) cc_final: 0.8045 (ttpt) REVERT: A 385 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7983 (mtpp) REVERT: A 388 SER cc_start: 0.8588 (t) cc_final: 0.8091 (p) REVERT: A 413 GLU cc_start: 0.7318 (tt0) cc_final: 0.7082 (tt0) REVERT: A 416 SER cc_start: 0.8942 (m) cc_final: 0.8465 (p) REVERT: A 427 ILE cc_start: 0.8078 (mt) cc_final: 0.7640 (tt) REVERT: A 430 ARG cc_start: 0.8089 (tpt170) cc_final: 0.7835 (tpt170) REVERT: A 433 GLU cc_start: 0.7779 (mp0) cc_final: 0.7097 (mp0) REVERT: A 437 TRP cc_start: 0.8222 (m100) cc_final: 0.7369 (m-10) REVERT: A 440 SER cc_start: 0.8371 (t) cc_final: 0.8088 (t) REVERT: A 453 TYR cc_start: 0.8076 (p90) cc_final: 0.7651 (p90) REVERT: H 13 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7293 (mtmm) REVERT: H 16 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7124 (mt-10) REVERT: H 99 TYR cc_start: 0.7927 (m-80) cc_final: 0.7556 (m-80) REVERT: H 100 LEU cc_start: 0.7995 (mt) cc_final: 0.7719 (mp) REVERT: L 7 SER cc_start: 0.8657 (m) cc_final: 0.8226 (p) REVERT: L 10 SER cc_start: 0.8025 (t) cc_final: 0.7758 (m) REVERT: L 42 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8106 (mmmt) REVERT: L 58 VAL cc_start: 0.8836 (t) cc_final: 0.8549 (p) REVERT: L 103 LYS cc_start: 0.7804 (tttt) cc_final: 0.7370 (tttt) REVERT: M 32 TYR cc_start: 0.7706 (m-80) cc_final: 0.7478 (m-10) REVERT: M 59 TYR cc_start: 0.8496 (m-80) cc_final: 0.7955 (m-80) REVERT: M 96 SER cc_start: 0.8269 (m) cc_final: 0.7998 (p) REVERT: N 56 SER cc_start: 0.8666 (t) cc_final: 0.8391 (p) REVERT: N 89 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7572 (tm-30) outliers start: 38 outliers final: 26 residues processed: 268 average time/residue: 0.1920 time to fit residues: 66.9222 Evaluate side-chains 276 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.090509 restraints weight = 11776.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.093682 restraints weight = 4911.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.095639 restraints weight = 2486.833| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6769 Z= 0.330 Angle : 0.694 8.932 9197 Z= 0.361 Chirality : 0.049 0.172 997 Planarity : 0.005 0.053 1179 Dihedral : 5.816 49.823 958 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 5.65 % Allowed : 19.56 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.27), residues: 841 helix: -2.68 (2.45), residues: 6 sheet: -1.06 (0.29), residues: 338 loop : -2.72 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 7 HIS 0.005 0.001 HIS N 90 PHE 0.030 0.002 PHE H 78 TYR 0.033 0.002 TYR N 49 ARG 0.005 0.001 ARG N 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8313 (mttt) cc_final: 0.7969 (mmtt) REVERT: A 187 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8283 (mtmt) REVERT: A 245 SER cc_start: 0.8522 (t) cc_final: 0.8111 (p) REVERT: A 251 ASP cc_start: 0.7638 (m-30) cc_final: 0.7317 (m-30) REVERT: A 261 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7810 (tmmm) REVERT: A 271 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8571 (p) REVERT: A 292 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7378 (ptt180) REVERT: A 302 ILE cc_start: 0.8752 (mt) cc_final: 0.8300 (mm) REVERT: A 307 VAL cc_start: 0.8620 (m) cc_final: 0.8332 (t) REVERT: A 309 ASN cc_start: 0.7690 (t0) cc_final: 0.7152 (t0) REVERT: A 343 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: A 370 LEU cc_start: 0.8776 (mt) cc_final: 0.8545 (mm) REVERT: A 375 GLU cc_start: 0.7590 (pt0) cc_final: 0.7112 (pt0) REVERT: A 378 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8050 (ttpt) REVERT: A 385 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8060 (mtpp) REVERT: A 388 SER cc_start: 0.8568 (t) cc_final: 0.7981 (p) REVERT: A 389 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8457 (mttt) REVERT: A 413 GLU cc_start: 0.7350 (tt0) cc_final: 0.7119 (tt0) REVERT: A 416 SER cc_start: 0.8951 (m) cc_final: 0.8437 (p) REVERT: A 427 ILE cc_start: 0.8179 (mt) cc_final: 0.7752 (tt) REVERT: A 430 ARG cc_start: 0.8154 (tpt170) cc_final: 0.7928 (tpt170) REVERT: A 433 GLU cc_start: 0.7804 (mp0) cc_final: 0.7106 (mp0) REVERT: A 437 TRP cc_start: 0.8258 (m100) cc_final: 0.7106 (m-10) REVERT: A 440 SER cc_start: 0.8412 (t) cc_final: 0.8112 (t) REVERT: A 453 TYR cc_start: 0.8097 (p90) cc_final: 0.7707 (p90) REVERT: H 13 LYS cc_start: 0.7798 (mtmm) cc_final: 0.7419 (mtmm) REVERT: H 16 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7280 (mt-10) REVERT: H 81 LYS cc_start: 0.8196 (mttt) cc_final: 0.7941 (mptt) REVERT: H 99 TYR cc_start: 0.7951 (m-80) cc_final: 0.7387 (m-80) REVERT: H 100 LEU cc_start: 0.8054 (mt) cc_final: 0.7823 (mp) REVERT: L 7 SER cc_start: 0.8741 (m) cc_final: 0.8304 (p) REVERT: L 10 SER cc_start: 0.8103 (t) cc_final: 0.7809 (m) REVERT: L 42 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8143 (mmmt) REVERT: L 58 VAL cc_start: 0.8865 (t) cc_final: 0.8555 (p) REVERT: L 103 LYS cc_start: 0.7940 (tttt) cc_final: 0.7472 (tttt) REVERT: M 32 TYR cc_start: 0.7819 (m-80) cc_final: 0.7596 (m-10) REVERT: M 96 SER cc_start: 0.8297 (m) cc_final: 0.8024 (p) REVERT: N 24 ARG cc_start: 0.7220 (ttm170) cc_final: 0.6888 (ttm170) REVERT: N 56 SER cc_start: 0.8642 (t) cc_final: 0.8345 (p) outliers start: 41 outliers final: 32 residues processed: 269 average time/residue: 0.1913 time to fit residues: 66.7697 Evaluate side-chains 287 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092918 restraints weight = 11800.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.096107 restraints weight = 4936.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.098083 restraints weight = 2500.263| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6769 Z= 0.224 Angle : 0.650 8.957 9197 Z= 0.336 Chirality : 0.048 0.182 997 Planarity : 0.005 0.046 1179 Dihedral : 5.582 48.211 958 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.41 % Allowed : 21.90 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.27), residues: 841 helix: -2.68 (2.37), residues: 6 sheet: -0.99 (0.28), residues: 347 loop : -2.55 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 7 HIS 0.003 0.001 HIS A 264 PHE 0.023 0.002 PHE A 410 TYR 0.032 0.002 TYR N 49 ARG 0.007 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8297 (mttt) cc_final: 0.7940 (mmtt) REVERT: A 104 ASN cc_start: 0.8261 (m110) cc_final: 0.7986 (m-40) REVERT: A 245 SER cc_start: 0.8494 (t) cc_final: 0.8101 (p) REVERT: A 251 ASP cc_start: 0.7551 (m-30) cc_final: 0.7207 (m-30) REVERT: A 261 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7786 (tmmm) REVERT: A 271 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8546 (p) REVERT: A 292 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7411 (ptt180) REVERT: A 302 ILE cc_start: 0.8759 (mt) cc_final: 0.8278 (mm) REVERT: A 307 VAL cc_start: 0.8562 (m) cc_final: 0.8259 (t) REVERT: A 309 ASN cc_start: 0.7678 (t0) cc_final: 0.7077 (t0) REVERT: A 343 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: A 370 LEU cc_start: 0.8774 (mt) cc_final: 0.8538 (mm) REVERT: A 375 GLU cc_start: 0.7566 (pt0) cc_final: 0.7126 (pt0) REVERT: A 378 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7928 (ttpt) REVERT: A 385 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8028 (mtpp) REVERT: A 388 SER cc_start: 0.8553 (t) cc_final: 0.8015 (p) REVERT: A 389 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8732 (mttm) REVERT: A 416 SER cc_start: 0.8947 (m) cc_final: 0.8446 (p) REVERT: A 427 ILE cc_start: 0.8138 (mt) cc_final: 0.7730 (tt) REVERT: A 430 ARG cc_start: 0.8133 (tpt170) cc_final: 0.7862 (tpt170) REVERT: A 433 GLU cc_start: 0.7790 (mp0) cc_final: 0.7118 (mp0) REVERT: A 437 TRP cc_start: 0.8226 (m100) cc_final: 0.7252 (m-10) REVERT: A 440 SER cc_start: 0.8424 (t) cc_final: 0.8134 (t) REVERT: A 453 TYR cc_start: 0.8091 (p90) cc_final: 0.7689 (p90) REVERT: H 13 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7370 (mtmm) REVERT: H 16 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7198 (mt-10) REVERT: H 29 PHE cc_start: 0.8097 (t80) cc_final: 0.7815 (m-80) REVERT: H 81 LYS cc_start: 0.8202 (mttt) cc_final: 0.7968 (mptt) REVERT: H 99 TYR cc_start: 0.7933 (m-80) cc_final: 0.7513 (m-80) REVERT: L 7 SER cc_start: 0.8700 (m) cc_final: 0.8260 (p) REVERT: L 10 SER cc_start: 0.8036 (t) cc_final: 0.7768 (m) REVERT: L 42 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8052 (mmmt) REVERT: L 58 VAL cc_start: 0.8868 (t) cc_final: 0.8561 (p) REVERT: L 103 LYS cc_start: 0.7934 (tttt) cc_final: 0.7469 (tttt) REVERT: M 32 TYR cc_start: 0.7754 (m-80) cc_final: 0.7532 (m-10) REVERT: M 59 TYR cc_start: 0.8460 (m-80) cc_final: 0.7907 (m-80) REVERT: M 96 SER cc_start: 0.8360 (m) cc_final: 0.8102 (p) REVERT: N 56 SER cc_start: 0.8659 (t) cc_final: 0.8370 (p) outliers start: 32 outliers final: 26 residues processed: 260 average time/residue: 0.1967 time to fit residues: 66.3306 Evaluate side-chains 273 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.104413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.092121 restraints weight = 11976.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.095341 restraints weight = 5026.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.097292 restraints weight = 2552.731| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6769 Z= 0.212 Angle : 0.658 8.874 9197 Z= 0.338 Chirality : 0.048 0.193 997 Planarity : 0.005 0.043 1179 Dihedral : 5.516 47.993 958 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.41 % Allowed : 22.87 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.28), residues: 841 helix: -2.85 (2.22), residues: 6 sheet: -0.83 (0.29), residues: 339 loop : -2.53 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 7 HIS 0.005 0.001 HIS A 274 PHE 0.027 0.002 PHE A 410 TYR 0.032 0.002 TYR N 49 ARG 0.003 0.000 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 244 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8251 (mttt) cc_final: 0.7972 (mmtt) REVERT: A 132 PHE cc_start: 0.7651 (m-80) cc_final: 0.7371 (m-80) REVERT: A 245 SER cc_start: 0.8493 (t) cc_final: 0.8222 (p) REVERT: A 251 ASP cc_start: 0.7539 (m-30) cc_final: 0.7265 (m-30) REVERT: A 261 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7784 (tmmm) REVERT: A 271 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8562 (p) REVERT: A 292 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7322 (ptt180) REVERT: A 302 ILE cc_start: 0.8744 (mt) cc_final: 0.8273 (mm) REVERT: A 307 VAL cc_start: 0.8540 (m) cc_final: 0.8240 (t) REVERT: A 309 ASN cc_start: 0.7665 (t0) cc_final: 0.7051 (t0) REVERT: A 343 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 370 LEU cc_start: 0.8759 (mt) cc_final: 0.8528 (mm) REVERT: A 375 GLU cc_start: 0.7585 (pt0) cc_final: 0.7103 (pt0) REVERT: A 378 LYS cc_start: 0.8181 (ttpt) cc_final: 0.7898 (ttpt) REVERT: A 385 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8025 (mtpp) REVERT: A 388 SER cc_start: 0.8543 (t) cc_final: 0.7972 (p) REVERT: A 389 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8431 (mttp) REVERT: A 399 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6739 (mt-10) REVERT: A 416 SER cc_start: 0.8948 (m) cc_final: 0.8453 (p) REVERT: A 427 ILE cc_start: 0.8122 (mt) cc_final: 0.7710 (tt) REVERT: A 430 ARG cc_start: 0.8134 (tpt170) cc_final: 0.7853 (tpt170) REVERT: A 433 GLU cc_start: 0.7742 (mp0) cc_final: 0.7062 (mp0) REVERT: A 437 TRP cc_start: 0.8229 (m100) cc_final: 0.7319 (m-10) REVERT: A 440 SER cc_start: 0.8424 (t) cc_final: 0.8114 (t) REVERT: A 453 TYR cc_start: 0.8091 (p90) cc_final: 0.7657 (p90) REVERT: H 13 LYS cc_start: 0.7723 (mtmm) cc_final: 0.7335 (mtmm) REVERT: H 16 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7110 (mt-10) REVERT: H 29 PHE cc_start: 0.8041 (t80) cc_final: 0.7758 (m-80) REVERT: H 99 TYR cc_start: 0.7948 (m-80) cc_final: 0.7523 (m-80) REVERT: L 7 SER cc_start: 0.8678 (m) cc_final: 0.8264 (p) REVERT: L 10 SER cc_start: 0.8000 (t) cc_final: 0.7738 (m) REVERT: L 42 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8030 (mmmt) REVERT: L 58 VAL cc_start: 0.8856 (t) cc_final: 0.8553 (p) REVERT: L 103 LYS cc_start: 0.7887 (tttt) cc_final: 0.7407 (tttt) REVERT: M 32 TYR cc_start: 0.7749 (m-80) cc_final: 0.7523 (m-10) REVERT: M 59 TYR cc_start: 0.8480 (m-80) cc_final: 0.7924 (m-80) REVERT: M 96 SER cc_start: 0.8363 (m) cc_final: 0.8102 (p) REVERT: N 56 SER cc_start: 0.8650 (t) cc_final: 0.8357 (p) outliers start: 32 outliers final: 27 residues processed: 256 average time/residue: 0.1963 time to fit residues: 65.6210 Evaluate side-chains 272 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.091649 restraints weight = 12150.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094869 restraints weight = 5088.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096761 restraints weight = 2577.067| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6769 Z= 0.249 Angle : 0.673 9.363 9197 Z= 0.348 Chirality : 0.048 0.193 997 Planarity : 0.005 0.048 1179 Dihedral : 5.564 47.233 958 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.82 % Allowed : 23.42 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.27), residues: 841 helix: -2.81 (2.30), residues: 6 sheet: -0.84 (0.29), residues: 336 loop : -2.55 (0.24), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 7 HIS 0.004 0.001 HIS A 274 PHE 0.028 0.002 PHE A 410 TYR 0.033 0.002 TYR N 49 ARG 0.003 0.000 ARG M 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8217 (mttt) cc_final: 0.7933 (mmtt) REVERT: A 132 PHE cc_start: 0.7676 (m-80) cc_final: 0.7400 (m-80) REVERT: A 187 LYS cc_start: 0.8509 (mttm) cc_final: 0.8180 (mtmm) REVERT: A 245 SER cc_start: 0.8498 (t) cc_final: 0.8118 (p) REVERT: A 251 ASP cc_start: 0.7539 (m-30) cc_final: 0.7252 (m-30) REVERT: A 261 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7822 (tmmm) REVERT: A 271 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8574 (p) REVERT: A 292 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7204 (ptt180) REVERT: A 302 ILE cc_start: 0.8743 (mt) cc_final: 0.8282 (mm) REVERT: A 307 VAL cc_start: 0.8554 (m) cc_final: 0.8270 (t) REVERT: A 309 ASN cc_start: 0.7644 (t0) cc_final: 0.7047 (t0) REVERT: A 343 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: A 370 LEU cc_start: 0.8779 (mt) cc_final: 0.8556 (mm) REVERT: A 378 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7835 (ttpt) REVERT: A 385 LYS cc_start: 0.8392 (mmmt) cc_final: 0.8033 (mtpp) REVERT: A 388 SER cc_start: 0.8571 (t) cc_final: 0.8003 (p) REVERT: A 389 LYS cc_start: 0.8910 (mtpp) cc_final: 0.8568 (mtpp) REVERT: A 399 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6759 (mt-10) REVERT: A 416 SER cc_start: 0.8963 (m) cc_final: 0.8481 (p) REVERT: A 427 ILE cc_start: 0.8133 (mt) cc_final: 0.7742 (tt) REVERT: A 430 ARG cc_start: 0.8137 (tpt170) cc_final: 0.7846 (tpt170) REVERT: A 433 GLU cc_start: 0.7739 (mp0) cc_final: 0.7065 (mp0) REVERT: A 437 TRP cc_start: 0.8236 (m100) cc_final: 0.7322 (m-10) REVERT: A 440 SER cc_start: 0.8416 (t) cc_final: 0.8088 (t) REVERT: A 453 TYR cc_start: 0.8086 (p90) cc_final: 0.7676 (p90) REVERT: H 13 LYS cc_start: 0.7758 (mtmm) cc_final: 0.7364 (mtmm) REVERT: H 16 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7171 (mt-10) REVERT: H 29 PHE cc_start: 0.8038 (t80) cc_final: 0.7732 (m-80) REVERT: H 81 LYS cc_start: 0.8322 (mttt) cc_final: 0.8064 (mptt) REVERT: H 99 TYR cc_start: 0.7947 (m-80) cc_final: 0.7512 (m-80) REVERT: L 7 SER cc_start: 0.8718 (m) cc_final: 0.8274 (p) REVERT: L 10 SER cc_start: 0.8007 (t) cc_final: 0.7738 (m) REVERT: L 24 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6890 (mmm160) REVERT: L 42 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8055 (mmmt) REVERT: L 58 VAL cc_start: 0.8861 (t) cc_final: 0.8557 (p) REVERT: L 103 LYS cc_start: 0.7971 (tttt) cc_final: 0.7474 (tttt) REVERT: M 32 TYR cc_start: 0.7772 (m-80) cc_final: 0.7525 (m-10) REVERT: M 59 TYR cc_start: 0.8483 (m-80) cc_final: 0.7910 (m-80) REVERT: M 96 SER cc_start: 0.8369 (m) cc_final: 0.8111 (p) REVERT: N 56 SER cc_start: 0.8648 (t) cc_final: 0.8361 (p) outliers start: 35 outliers final: 29 residues processed: 258 average time/residue: 0.1922 time to fit residues: 64.3197 Evaluate side-chains 275 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 242 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.106633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.094554 restraints weight = 12074.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097676 restraints weight = 5111.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099593 restraints weight = 2602.998| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6769 Z= 0.174 Angle : 0.632 9.105 9197 Z= 0.326 Chirality : 0.047 0.189 997 Planarity : 0.004 0.043 1179 Dihedral : 5.245 45.614 958 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.13 % Allowed : 24.10 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.27), residues: 841 helix: -2.96 (2.04), residues: 6 sheet: -0.69 (0.30), residues: 316 loop : -2.38 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 7 HIS 0.004 0.001 HIS A 274 PHE 0.026 0.001 PHE A 410 TYR 0.031 0.001 TYR N 49 ARG 0.003 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.26 seconds wall clock time: 46 minutes 51.04 seconds (2811.04 seconds total)