Starting phenix.real_space_refine on Sun Apr 27 21:50:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gau_29908/04_2025/8gau_29908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gau_29908/04_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_29908/04_2025/8gau_29908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gau_29908/04_2025/8gau_29908.map" model { file = "/net/cci-nas-00/data/ceres_data/8gau_29908/04_2025/8gau_29908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gau_29908/04_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-5669/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: 4.40, per 1000 atoms: 0.67 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: 1.51 Conformation dependent library (CDL) restraints added in 988.1 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: 0.86 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: 2.14 Time building geometry restraints manager: 1.86 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: 0.430 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- 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 6783 Z= 0.324 Angle : 1.056 12.196 9226 Z= 0.610 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00772 ( 1) link_NAG-ASN : angle 4.22272 ( 3) hydrogen bonds : bond 0.27695 ( 151) hydrogen bonds : angle 10.22531 ( 423) SS BOND : bond 0.00979 ( 13) SS BOND : angle 2.94023 ( 26) covalent geometry : bond 0.00616 ( 6769) covalent geometry : angle 1.04374 ( 9197) *********************** 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 : 0.668 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: 0.1819 time to fit residues: 72.0914 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 : 0.655 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 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: 0.8784 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.106093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093570 restraints weight = 11678.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096793 restraints weight = 4925.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098759 restraints weight = 2517.854| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6783 Z= 0.147 Angle : 0.660 8.473 9226 Z= 0.346 Chirality : 0.047 0.159 997 Planarity : 0.006 0.052 1179 Dihedral : 6.495 59.022 959 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 3.31 % Allowed : 11.98 % Favored : 84.71 % 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: -3.56 (0.26), residues: 841 helix: -4.35 (0.52), residues: 6 sheet: -1.60 (0.29), residues: 318 loop : -2.99 (0.23), residues: 517 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 0.014 0.002 PHE H 78 TYR 0.021 0.002 TYR M 100A ARG 0.005 0.001 ARG M 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 1) link_NAG-ASN : angle 3.21159 ( 3) hydrogen bonds : bond 0.04323 ( 151) hydrogen bonds : angle 6.62371 ( 423) SS BOND : bond 0.00406 ( 13) SS BOND : angle 1.03039 ( 26) covalent geometry : bond 0.00312 ( 6769) covalent geometry : angle 0.65577 ( 9197) *********************** 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 282 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8275 (mttt) cc_final: 0.7882 (mmtt) REVERT: A 104 ASN cc_start: 0.8329 (m-40) cc_final: 0.7966 (m110) REVERT: A 128 LYS cc_start: 0.8023 (pttm) cc_final: 0.7336 (pttm) REVERT: A 142 ASN cc_start: 0.8024 (t0) cc_final: 0.7767 (t0) REVERT: A 162 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7329 (mt-10) REVERT: A 245 SER cc_start: 0.8512 (t) cc_final: 0.7910 (p) REVERT: A 251 ASP cc_start: 0.7536 (m-30) cc_final: 0.7195 (m-30) REVERT: A 258 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6861 (mt-10) REVERT: A 261 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7576 (tmmm) REVERT: A 276 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6675 (mm-30) REVERT: A 292 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7299 (ptt180) REVERT: A 302 ILE cc_start: 0.8623 (mt) cc_final: 0.8156 (mm) REVERT: A 327 ARG cc_start: 0.8302 (ptt-90) cc_final: 0.8081 (ptt-90) REVERT: A 343 GLU cc_start: 0.7388 (mp0) cc_final: 0.6858 (mp0) REVERT: A 356 ASP cc_start: 0.8236 (t0) cc_final: 0.8027 (t0) REVERT: A 370 LEU cc_start: 0.8703 (mt) cc_final: 0.8375 (mm) REVERT: A 375 GLU cc_start: 0.7653 (pt0) cc_final: 0.7078 (pt0) REVERT: A 378 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7951 (ttpt) REVERT: A 381 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7073 (mm-30) REVERT: A 385 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8024 (mtpp) REVERT: A 388 SER cc_start: 0.8431 (t) cc_final: 0.7981 (p) REVERT: A 389 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8701 (mtpp) REVERT: A 399 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6758 (mt-10) REVERT: A 413 GLU cc_start: 0.7296 (tt0) cc_final: 0.7058 (tt0) REVERT: A 416 SER cc_start: 0.8910 (m) cc_final: 0.8410 (p) REVERT: A 427 ILE cc_start: 0.8194 (mt) cc_final: 0.7791 (tp) REVERT: A 433 GLU cc_start: 0.7657 (mp0) cc_final: 0.6973 (mp0) REVERT: A 437 TRP cc_start: 0.8353 (m100) cc_final: 0.7536 (m-10) REVERT: A 453 TYR cc_start: 0.7895 (p90) cc_final: 0.7688 (p90) REVERT: A 463 ASP cc_start: 0.8005 (t0) cc_final: 0.7796 (t0) REVERT: H 7 TRP cc_start: 0.7569 (p-90) cc_final: 0.7363 (p-90) REVERT: H 13 LYS cc_start: 0.7682 (mtmm) cc_final: 0.7423 (mtmm) REVERT: H 25 TYR cc_start: 0.7919 (m-80) cc_final: 0.7701 (m-10) REVERT: H 31 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6851 (p90) REVERT: H 100 HIS cc_start: 0.7404 (t-90) cc_final: 0.6946 (t-90) REVERT: H 100 LEU cc_start: 0.8088 (mt) cc_final: 0.7420 (mt) REVERT: H 100 TYR cc_start: 0.8065 (m-80) cc_final: 0.7518 (m-80) REVERT: L 4 MET cc_start: 0.5577 (mpp) cc_final: 0.5362 (mpp) REVERT: L 7 SER cc_start: 0.8634 (m) cc_final: 0.8229 (p) REVERT: L 58 VAL cc_start: 0.8802 (t) cc_final: 0.8511 (p) REVERT: L 103 LYS cc_start: 0.7752 (tttt) cc_final: 0.7284 (tttt) REVERT: L 107 LYS cc_start: 0.7779 (pttp) cc_final: 0.7236 (tppt) REVERT: M 32 TYR cc_start: 0.7733 (m-80) cc_final: 0.7442 (m-10) REVERT: M 59 TYR cc_start: 0.8215 (m-10) cc_final: 0.7851 (m-80) REVERT: M 96 SER cc_start: 0.8377 (m) cc_final: 0.7998 (p) REVERT: N 56 SER cc_start: 0.8645 (t) cc_final: 0.8268 (p) REVERT: N 67 TYR cc_start: 0.8320 (t80) cc_final: 0.8064 (t80) REVERT: N 82 ASP cc_start: 0.8192 (m-30) cc_final: 0.7726 (m-30) REVERT: N 86 TYR cc_start: 0.8105 (m-10) cc_final: 0.7454 (m-80) outliers start: 24 outliers final: 15 residues processed: 268 average time/residue: 0.2003 time to fit residues: 69.5766 Evaluate side-chains 258 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 398 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 82 VAL 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 M residue 57 THR 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: 1.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 52 optimal weight: 3.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- 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 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3284 r_free = 0.3284 target = 0.102970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.090558 restraints weight = 11847.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.093773 restraints weight = 4942.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.095722 restraints weight = 2502.612| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6783 Z= 0.240 Angle : 0.711 8.339 9226 Z= 0.372 Chirality : 0.048 0.154 997 Planarity : 0.006 0.056 1179 Dihedral : 6.289 49.102 958 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % 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: -3.45 (0.26), residues: 841 helix: -3.74 (1.31), residues: 6 sheet: -1.51 (0.28), residues: 330 loop : -2.96 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 7 HIS 0.005 0.001 HIS A 264 PHE 0.025 0.002 PHE H 78 TYR 0.029 0.002 TYR N 49 ARG 0.005 0.001 ARG M 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 1) link_NAG-ASN : angle 3.80217 ( 3) hydrogen bonds : bond 0.04863 ( 151) hydrogen bonds : angle 6.25559 ( 423) SS BOND : bond 0.00495 ( 13) SS BOND : angle 1.33705 ( 26) covalent geometry : bond 0.00516 ( 6769) covalent geometry : angle 0.70507 ( 9197) *********************** 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 288 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8347 (mttt) cc_final: 0.7976 (mmtt) REVERT: A 104 ASN cc_start: 0.8327 (m-40) cc_final: 0.8009 (m-40) REVERT: A 128 LYS cc_start: 0.8020 (pttm) cc_final: 0.7699 (pttm) REVERT: A 245 SER cc_start: 0.8524 (t) cc_final: 0.8027 (p) REVERT: A 249 LYS cc_start: 0.8424 (mttt) cc_final: 0.7887 (mttt) REVERT: A 251 ASP cc_start: 0.7578 (m-30) cc_final: 0.7276 (m-30) REVERT: A 276 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6757 (mm-30) REVERT: A 292 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7212 (ptt180) REVERT: A 302 ILE cc_start: 0.8746 (mt) cc_final: 0.8263 (mm) REVERT: A 307 VAL cc_start: 0.8673 (m) cc_final: 0.8388 (t) REVERT: A 309 ASN cc_start: 0.7700 (t0) cc_final: 0.7352 (t0) REVERT: A 327 ARG cc_start: 0.8307 (ptt-90) cc_final: 0.8106 (ptt-90) REVERT: A 343 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: A 356 ASP cc_start: 0.8309 (t0) cc_final: 0.8095 (t0) REVERT: A 370 LEU cc_start: 0.8778 (mt) cc_final: 0.8553 (mm) REVERT: A 375 GLU cc_start: 0.7623 (pt0) cc_final: 0.7106 (pt0) REVERT: A 378 LYS cc_start: 0.8285 (ttpt) cc_final: 0.8078 (ttpt) REVERT: A 385 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8029 (mtpp) REVERT: A 388 SER cc_start: 0.8556 (t) cc_final: 0.8024 (p) REVERT: A 389 LYS cc_start: 0.8961 (mtpp) cc_final: 0.8587 (mtpp) REVERT: A 413 GLU cc_start: 0.7332 (tt0) cc_final: 0.7039 (tt0) REVERT: A 427 ILE cc_start: 0.8310 (mt) cc_final: 0.7874 (tt) REVERT: A 433 GLU cc_start: 0.7705 (mp0) cc_final: 0.7066 (mp0) REVERT: A 437 TRP cc_start: 0.8360 (m100) cc_final: 0.7466 (m-10) REVERT: A 440 SER cc_start: 0.8552 (t) cc_final: 0.8316 (t) REVERT: A 453 TYR cc_start: 0.8027 (p90) cc_final: 0.7734 (p90) REVERT: H 7 TRP cc_start: 0.7611 (p-90) cc_final: 0.7257 (p-90) REVERT: H 13 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7387 (mtmm) REVERT: H 16 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7322 (mt-10) REVERT: H 21 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7960 (p) REVERT: H 81 LYS cc_start: 0.8162 (mttt) cc_final: 0.7881 (mptt) REVERT: H 99 TYR cc_start: 0.7922 (m-80) cc_final: 0.7456 (m-80) REVERT: H 100 LEU cc_start: 0.8257 (mt) cc_final: 0.7920 (mp) REVERT: L 7 SER cc_start: 0.8806 (m) cc_final: 0.8341 (p) REVERT: L 22 THR cc_start: 0.7805 (p) cc_final: 0.7451 (p) REVERT: L 58 VAL cc_start: 0.8834 (t) cc_final: 0.8546 (p) REVERT: L 103 LYS cc_start: 0.7908 (tttt) cc_final: 0.7368 (tttt) REVERT: M 32 TYR cc_start: 0.7881 (m-80) cc_final: 0.7511 (m-10) REVERT: N 56 SER cc_start: 0.8658 (t) cc_final: 0.8304 (p) REVERT: N 67 TYR cc_start: 0.8354 (t80) cc_final: 0.8136 (t80) REVERT: N 82 ASP cc_start: 0.8215 (m-30) cc_final: 0.7996 (m-30) REVERT: N 86 TYR cc_start: 0.8073 (m-10) cc_final: 0.7539 (m-80) outliers start: 34 outliers final: 22 residues processed: 268 average time/residue: 0.1983 time to fit residues: 69.3866 Evaluate side-chains 266 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 271 SER 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 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: 2.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.0010 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 299 ASN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093644 restraints weight = 11899.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096850 restraints weight = 4945.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098809 restraints weight = 2499.559| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6783 Z= 0.122 Angle : 0.618 8.745 9226 Z= 0.319 Chirality : 0.046 0.173 997 Planarity : 0.004 0.045 1179 Dihedral : 5.466 46.147 954 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.55 % Allowed : 16.94 % Favored : 78.51 % 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: -2.97 (0.27), residues: 841 helix: -2.88 (2.09), residues: 6 sheet: -1.17 (0.29), residues: 334 loop : -2.65 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 52A HIS 0.001 0.001 HIS A 184 PHE 0.018 0.001 PHE A 410 TYR 0.029 0.002 TYR N 49 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 1) link_NAG-ASN : angle 2.71224 ( 3) hydrogen bonds : bond 0.03527 ( 151) hydrogen bonds : angle 5.75041 ( 423) SS BOND : bond 0.00387 ( 13) SS BOND : angle 1.00795 ( 26) covalent geometry : bond 0.00266 ( 6769) covalent geometry : angle 0.61512 ( 9197) *********************** 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 282 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8305 (mttt) cc_final: 0.7900 (mmtt) REVERT: A 104 ASN cc_start: 0.8290 (m-40) cc_final: 0.8048 (m-40) REVERT: A 128 LYS cc_start: 0.8036 (pttm) cc_final: 0.7766 (pttm) REVERT: A 142 ASN cc_start: 0.7951 (t0) cc_final: 0.7746 (t0) REVERT: A 245 SER cc_start: 0.8482 (t) cc_final: 0.7999 (p) REVERT: A 249 LYS cc_start: 0.8403 (mttt) cc_final: 0.7722 (mtpp) REVERT: A 251 ASP cc_start: 0.7637 (m-30) cc_final: 0.7380 (m-30) REVERT: A 271 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8597 (p) REVERT: A 276 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6742 (mm-30) REVERT: A 292 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7226 (ptt180) REVERT: A 302 ILE cc_start: 0.8645 (mt) cc_final: 0.8133 (mm) REVERT: A 306 ASN cc_start: 0.7904 (t0) cc_final: 0.7570 (t0) REVERT: A 307 VAL cc_start: 0.8594 (m) cc_final: 0.8150 (t) REVERT: A 309 ASN cc_start: 0.7784 (t0) cc_final: 0.7379 (t0) REVERT: A 316 TYR cc_start: 0.8055 (m-10) cc_final: 0.7679 (m-10) REVERT: A 343 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: A 356 ASP cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: A 370 LEU cc_start: 0.8760 (mt) cc_final: 0.8534 (mm) REVERT: A 375 GLU cc_start: 0.7577 (pt0) cc_final: 0.7099 (pt0) REVERT: A 378 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8069 (ttpt) REVERT: A 385 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8040 (mtpp) REVERT: A 388 SER cc_start: 0.8623 (t) cc_final: 0.8084 (p) REVERT: A 389 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8442 (mttp) REVERT: A 413 GLU cc_start: 0.7286 (tt0) cc_final: 0.7002 (tt0) REVERT: A 416 SER cc_start: 0.8940 (m) cc_final: 0.8463 (p) REVERT: A 427 ILE cc_start: 0.8210 (mt) cc_final: 0.7766 (tt) REVERT: A 433 GLU cc_start: 0.7804 (mp0) cc_final: 0.7197 (mp0) REVERT: A 437 TRP cc_start: 0.8327 (m100) cc_final: 0.7494 (m-10) REVERT: A 440 SER cc_start: 0.8477 (t) cc_final: 0.8215 (t) REVERT: A 453 TYR cc_start: 0.8079 (p90) cc_final: 0.7736 (p90) REVERT: H 7 TRP cc_start: 0.7497 (p-90) cc_final: 0.7177 (p-90) REVERT: H 13 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7358 (mtmm) REVERT: H 16 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7220 (mt-10) REVERT: H 81 LYS cc_start: 0.8137 (mttt) cc_final: 0.7917 (mptt) REVERT: H 99 TYR cc_start: 0.7896 (m-80) cc_final: 0.7533 (m-80) REVERT: H 100 LEU cc_start: 0.8041 (mt) cc_final: 0.7739 (mp) REVERT: L 7 SER cc_start: 0.8696 (m) cc_final: 0.8266 (p) REVERT: L 58 VAL cc_start: 0.8847 (t) cc_final: 0.8554 (p) REVERT: L 103 LYS cc_start: 0.7820 (tttt) cc_final: 0.7249 (tttt) REVERT: M 32 TYR cc_start: 0.7712 (m-80) cc_final: 0.7494 (m-10) REVERT: M 59 TYR cc_start: 0.8521 (m-80) cc_final: 0.8095 (m-80) REVERT: M 83 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8156 (ttmm) REVERT: M 96 SER cc_start: 0.8235 (m) cc_final: 0.8026 (p) REVERT: M 100 TYR cc_start: 0.7684 (t80) cc_final: 0.7482 (t80) REVERT: N 56 SER cc_start: 0.8630 (t) cc_final: 0.8329 (p) REVERT: N 67 TYR cc_start: 0.8404 (t80) cc_final: 0.7931 (t80) outliers start: 33 outliers final: 23 residues processed: 263 average time/residue: 0.2035 time to fit residues: 69.8456 Evaluate side-chains 269 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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 31 PHE Chi-restraints excluded: chain H residue 53 HIS 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 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 37 GLN 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: 0.9990 chunk 55 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 226 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.092182 restraints weight = 11731.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095367 restraints weight = 4877.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097228 restraints weight = 2457.208| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6783 Z= 0.153 Angle : 0.629 8.483 9226 Z= 0.324 Chirality : 0.047 0.165 997 Planarity : 0.005 0.048 1179 Dihedral : 5.387 41.550 954 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.68 % Allowed : 18.46 % Favored : 76.86 % 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: -2.91 (0.27), residues: 841 helix: -2.75 (2.24), residues: 6 sheet: -1.02 (0.28), residues: 348 loop : -2.73 (0.24), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.003 0.001 HIS N 90 PHE 0.022 0.002 PHE H 78 TYR 0.031 0.002 TYR N 49 ARG 0.005 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00176 ( 1) link_NAG-ASN : angle 2.93108 ( 3) hydrogen bonds : bond 0.03823 ( 151) hydrogen bonds : angle 5.72368 ( 423) SS BOND : bond 0.00384 ( 13) SS BOND : angle 1.06598 ( 26) covalent geometry : bond 0.00333 ( 6769) covalent geometry : angle 0.62561 ( 9197) *********************** 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 283 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 249 time to evaluate : 0.681 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: A 89 LYS cc_start: 0.8321 (mttt) cc_final: 0.7947 (mmtt) REVERT: A 104 ASN cc_start: 0.8328 (m-40) cc_final: 0.7987 (m-40) REVERT: A 128 LYS cc_start: 0.8045 (pttm) cc_final: 0.7762 (pttm) REVERT: A 142 ASN cc_start: 0.7868 (t0) cc_final: 0.7579 (t0) REVERT: A 245 SER cc_start: 0.8536 (t) cc_final: 0.8072 (p) REVERT: A 249 LYS cc_start: 0.8454 (mttt) cc_final: 0.8242 (mttt) REVERT: A 251 ASP cc_start: 0.7680 (m-30) cc_final: 0.7346 (m-30) REVERT: A 271 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 276 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6745 (mm-30) REVERT: A 292 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7366 (ptt180) REVERT: A 302 ILE cc_start: 0.8721 (mt) cc_final: 0.8221 (mm) REVERT: A 307 VAL cc_start: 0.8592 (m) cc_final: 0.8271 (t) REVERT: A 309 ASN cc_start: 0.7834 (t0) cc_final: 0.7388 (t0) REVERT: A 316 TYR cc_start: 0.8005 (m-10) cc_final: 0.7633 (m-10) REVERT: A 343 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: A 356 ASP cc_start: 0.8226 (t0) cc_final: 0.8016 (t0) REVERT: A 370 LEU cc_start: 0.8753 (mt) cc_final: 0.8513 (mm) REVERT: A 375 GLU cc_start: 0.7623 (pt0) cc_final: 0.7084 (pt0) REVERT: A 378 LYS cc_start: 0.8259 (ttpt) cc_final: 0.8036 (ttpt) REVERT: A 385 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8040 (mtpp) REVERT: A 388 SER cc_start: 0.8614 (t) cc_final: 0.8075 (p) REVERT: A 389 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8711 (mttm) REVERT: A 413 GLU cc_start: 0.7306 (tt0) cc_final: 0.7033 (tt0) REVERT: A 416 SER cc_start: 0.8952 (m) cc_final: 0.8441 (p) REVERT: A 427 ILE cc_start: 0.8166 (mt) cc_final: 0.7728 (tt) REVERT: A 433 GLU cc_start: 0.7783 (mp0) cc_final: 0.7125 (mp0) REVERT: A 437 TRP cc_start: 0.8347 (m100) cc_final: 0.7412 (m-10) REVERT: A 440 SER cc_start: 0.8471 (t) cc_final: 0.8197 (t) REVERT: A 453 TYR cc_start: 0.8083 (p90) cc_final: 0.7651 (p90) REVERT: H 7 TRP cc_start: 0.7545 (p-90) cc_final: 0.7248 (p-90) REVERT: H 13 LYS cc_start: 0.7680 (mtmm) cc_final: 0.7341 (mtmm) REVERT: H 16 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7248 (mt-10) REVERT: H 81 LYS cc_start: 0.8141 (mttt) cc_final: 0.7914 (mptt) REVERT: H 99 TYR cc_start: 0.7925 (m-80) cc_final: 0.7500 (m-80) REVERT: H 100 LEU cc_start: 0.8003 (mt) cc_final: 0.7730 (mp) REVERT: L 7 SER cc_start: 0.8705 (m) cc_final: 0.8265 (p) REVERT: L 45 LYS cc_start: 0.8319 (tttt) cc_final: 0.8085 (tttt) REVERT: L 58 VAL cc_start: 0.8845 (t) cc_final: 0.8543 (p) REVERT: L 103 LYS cc_start: 0.7832 (tttt) cc_final: 0.7280 (tttt) REVERT: M 59 TYR cc_start: 0.8510 (m-80) cc_final: 0.7970 (m-80) REVERT: M 83 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8187 (ttmm) REVERT: N 24 ARG cc_start: 0.7173 (ttm170) cc_final: 0.6905 (ttm170) REVERT: N 56 SER cc_start: 0.8637 (t) cc_final: 0.8327 (p) REVERT: N 67 TYR cc_start: 0.8420 (t80) cc_final: 0.7964 (t80) REVERT: N 89 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7201 (tt0) outliers start: 34 outliers final: 25 residues processed: 260 average time/residue: 0.1904 time to fit residues: 64.2355 Evaluate side-chains 272 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 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 53 HIS 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 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 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU 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 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** N 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093761 restraints weight = 11675.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.096964 restraints weight = 4868.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098891 restraints weight = 2470.158| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6783 Z= 0.105 Angle : 0.600 8.313 9226 Z= 0.303 Chirality : 0.046 0.169 997 Planarity : 0.004 0.041 1179 Dihedral : 5.085 42.834 954 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.99 % Allowed : 19.70 % 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: -2.62 (0.28), residues: 841 helix: -2.57 (2.42), residues: 6 sheet: -0.77 (0.29), residues: 339 loop : -2.55 (0.25), residues: 496 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 0.016 0.001 PHE H 78 TYR 0.030 0.001 TYR N 49 ARG 0.007 0.000 ARG M 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 2.31558 ( 3) hydrogen bonds : bond 0.03122 ( 151) hydrogen bonds : angle 5.46529 ( 423) SS BOND : bond 0.00322 ( 13) SS BOND : angle 0.85889 ( 26) covalent geometry : bond 0.00233 ( 6769) covalent geometry : angle 0.59742 ( 9197) *********************** 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 276 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.662 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: 0.8287 (mttt) cc_final: 0.7882 (mmtt) REVERT: A 104 ASN cc_start: 0.8305 (m-40) cc_final: 0.8083 (m110) REVERT: A 128 LYS cc_start: 0.8016 (pttm) cc_final: 0.7758 (pttm) REVERT: A 142 ASN cc_start: 0.7881 (t0) cc_final: 0.7654 (t0) REVERT: A 245 SER cc_start: 0.8453 (t) cc_final: 0.8126 (p) REVERT: A 249 LYS cc_start: 0.8422 (mttt) cc_final: 0.8006 (mttt) REVERT: A 251 ASP cc_start: 0.7677 (m-30) cc_final: 0.7431 (m-30) REVERT: A 276 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6736 (mm-30) REVERT: A 292 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7394 (ptt180) REVERT: A 302 ILE cc_start: 0.8697 (mt) cc_final: 0.8183 (mm) REVERT: A 307 VAL cc_start: 0.8549 (m) cc_final: 0.8226 (t) REVERT: A 309 ASN cc_start: 0.7821 (t0) cc_final: 0.7360 (t0) REVERT: A 316 TYR cc_start: 0.8008 (m-10) cc_final: 0.7709 (m-10) REVERT: A 343 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: A 356 ASP cc_start: 0.8184 (t0) cc_final: 0.7963 (t0) REVERT: A 370 LEU cc_start: 0.8713 (mt) cc_final: 0.8487 (mm) REVERT: A 375 GLU cc_start: 0.7633 (pt0) cc_final: 0.7114 (pt0) REVERT: A 378 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7931 (ttpt) REVERT: A 385 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7979 (mtpp) REVERT: A 388 SER cc_start: 0.8597 (t) cc_final: 0.8041 (p) REVERT: A 389 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8538 (mttm) REVERT: A 399 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 413 GLU cc_start: 0.7343 (tt0) cc_final: 0.7108 (tt0) REVERT: A 416 SER cc_start: 0.8938 (m) cc_final: 0.8459 (p) REVERT: A 427 ILE cc_start: 0.8113 (mt) cc_final: 0.7681 (tt) REVERT: A 433 GLU cc_start: 0.7762 (mp0) cc_final: 0.7145 (mp0) REVERT: A 437 TRP cc_start: 0.8299 (m100) cc_final: 0.7379 (m-10) REVERT: A 440 SER cc_start: 0.8378 (t) cc_final: 0.8075 (t) REVERT: A 453 TYR cc_start: 0.8066 (p90) cc_final: 0.7704 (p90) REVERT: H 13 LYS cc_start: 0.7607 (mtmm) cc_final: 0.7263 (mtmm) REVERT: H 16 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7037 (mt-10) REVERT: H 29 PHE cc_start: 0.8138 (t80) cc_final: 0.7890 (m-80) REVERT: H 59 TYR cc_start: 0.7664 (m-10) cc_final: 0.7430 (m-10) REVERT: H 78 PHE cc_start: 0.7627 (p90) cc_final: 0.7366 (p90) REVERT: L 7 SER cc_start: 0.8622 (m) cc_final: 0.8205 (p) REVERT: L 10 SER cc_start: 0.8021 (t) cc_final: 0.7750 (m) REVERT: L 42 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8170 (mmmt) REVERT: L 58 VAL cc_start: 0.8819 (t) cc_final: 0.8530 (p) REVERT: L 103 LYS cc_start: 0.7811 (tttt) cc_final: 0.7373 (tttt) REVERT: M 59 TYR cc_start: 0.8557 (m-80) cc_final: 0.7986 (m-80) REVERT: N 56 SER cc_start: 0.8683 (t) cc_final: 0.8424 (p) outliers start: 29 outliers final: 23 residues processed: 258 average time/residue: 0.2004 time to fit residues: 68.6221 Evaluate side-chains 266 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 241 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 20 LEU Chi-restraints excluded: chain H residue 24 VAL 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 67 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 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 100 PHE 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: 2.9990 chunk 55 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 347 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.090271 restraints weight = 11813.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093457 restraints weight = 4938.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095400 restraints weight = 2504.594| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6783 Z= 0.259 Angle : 0.723 9.267 9226 Z= 0.373 Chirality : 0.049 0.174 997 Planarity : 0.005 0.056 1179 Dihedral : 5.687 37.303 954 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.58 % Favored : 89.42 % Rotamer: Outliers : 4.96 % Allowed : 19.70 % Favored : 75.34 % 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: -2.94 (0.27), residues: 841 helix: -2.63 (2.51), residues: 6 sheet: -1.11 (0.28), residues: 339 loop : -2.68 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP H 7 HIS 0.005 0.001 HIS N 90 PHE 0.029 0.002 PHE H 78 TYR 0.036 0.002 TYR N 49 ARG 0.006 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 1) link_NAG-ASN : angle 3.54596 ( 3) hydrogen bonds : bond 0.04572 ( 151) hydrogen bonds : angle 5.95798 ( 423) SS BOND : bond 0.00529 ( 13) SS BOND : angle 1.26802 ( 26) covalent geometry : bond 0.00560 ( 6769) covalent geometry : angle 0.71800 ( 9197) *********************** 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 290 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8322 (mttt) cc_final: 0.7942 (mmtt) REVERT: A 128 LYS cc_start: 0.8093 (pttm) cc_final: 0.7799 (pttm) REVERT: A 142 ASN cc_start: 0.7888 (t0) cc_final: 0.7687 (t0) REVERT: A 251 ASP cc_start: 0.7662 (m-30) cc_final: 0.7322 (m-30) REVERT: A 292 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7158 (ptt180) REVERT: A 302 ILE cc_start: 0.8715 (mt) cc_final: 0.8256 (mm) REVERT: A 307 VAL cc_start: 0.8643 (m) cc_final: 0.8378 (t) REVERT: A 309 ASN cc_start: 0.7815 (t0) cc_final: 0.7336 (t0) REVERT: A 343 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: A 370 LEU cc_start: 0.8778 (mt) cc_final: 0.8535 (mm) REVERT: A 375 GLU cc_start: 0.7657 (pt0) cc_final: 0.7065 (pt0) REVERT: A 378 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7949 (ttpt) REVERT: A 385 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8046 (mtpp) REVERT: A 388 SER cc_start: 0.8526 (t) cc_final: 0.7940 (p) REVERT: A 389 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8423 (mttt) REVERT: A 399 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6724 (mt-10) REVERT: A 413 GLU cc_start: 0.7373 (tt0) cc_final: 0.7130 (tt0) REVERT: A 416 SER cc_start: 0.8947 (m) cc_final: 0.8456 (p) REVERT: A 419 ASN cc_start: 0.8090 (t0) cc_final: 0.7888 (t0) REVERT: A 427 ILE cc_start: 0.8238 (mt) cc_final: 0.7813 (tt) REVERT: A 433 GLU cc_start: 0.7734 (mp0) cc_final: 0.7070 (mp0) REVERT: A 437 TRP cc_start: 0.8325 (m100) cc_final: 0.7297 (m-10) REVERT: A 440 SER cc_start: 0.8482 (t) cc_final: 0.8171 (t) REVERT: A 453 TYR cc_start: 0.8098 (p90) cc_final: 0.7703 (p90) REVERT: H 13 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7434 (mtmm) REVERT: H 16 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7332 (mt-10) REVERT: H 50 GLU cc_start: 0.7278 (pt0) cc_final: 0.7013 (pt0) REVERT: H 81 LYS cc_start: 0.8163 (mttt) cc_final: 0.7905 (mptt) REVERT: H 99 TYR cc_start: 0.7953 (m-80) cc_final: 0.7395 (m-80) REVERT: L 7 SER cc_start: 0.8781 (m) cc_final: 0.8326 (p) REVERT: L 10 SER cc_start: 0.8112 (t) cc_final: 0.7813 (m) REVERT: L 42 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8077 (mmmt) REVERT: L 58 VAL cc_start: 0.8865 (t) cc_final: 0.8545 (p) REVERT: L 103 LYS cc_start: 0.7857 (tttt) cc_final: 0.7390 (tttt) REVERT: M 100 PHE cc_start: 0.8417 (m-80) cc_final: 0.7952 (m-80) REVERT: N 24 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6786 (ttm-80) REVERT: N 56 SER cc_start: 0.8651 (t) cc_final: 0.8345 (p) outliers start: 36 outliers final: 31 residues processed: 269 average time/residue: 0.1911 time to fit residues: 66.7538 Evaluate side-chains 280 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 247 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 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 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 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 THR Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 27 GLN 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: 3.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 104 ASN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.092680 restraints weight = 11793.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095920 restraints weight = 4940.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.097872 restraints weight = 2509.201| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6783 Z= 0.145 Angle : 0.650 8.860 9226 Z= 0.334 Chirality : 0.048 0.178 997 Planarity : 0.005 0.046 1179 Dihedral : 5.344 39.163 954 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 4.41 % Allowed : 21.63 % Favored : 73.97 % 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: -2.74 (0.27), residues: 841 helix: -2.40 (2.65), residues: 6 sheet: -0.97 (0.28), residues: 347 loop : -2.56 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 1) link_NAG-ASN : angle 2.73756 ( 3) hydrogen bonds : bond 0.03664 ( 151) hydrogen bonds : angle 5.72869 ( 423) SS BOND : bond 0.00461 ( 13) SS BOND : angle 1.34498 ( 26) covalent geometry : bond 0.00318 ( 6769) covalent geometry : angle 0.64557 ( 9197) *********************** 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 282 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 250 time to evaluate : 0.707 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: 0.7873 (mmtt) REVERT: A 128 LYS cc_start: 0.8158 (pttm) cc_final: 0.7834 (pttm) REVERT: A 132 PHE cc_start: 0.7643 (m-80) cc_final: 0.7326 (m-80) REVERT: A 245 SER cc_start: 0.8512 (t) cc_final: 0.8104 (p) REVERT: A 251 ASP cc_start: 0.7577 (m-30) cc_final: 0.7263 (m-30) REVERT: A 262 ILE cc_start: 0.8558 (mt) cc_final: 0.8307 (tt) REVERT: A 292 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7383 (ptt180) REVERT: A 302 ILE cc_start: 0.8738 (mt) cc_final: 0.8276 (mm) REVERT: A 307 VAL cc_start: 0.8583 (m) cc_final: 0.8284 (t) REVERT: A 309 ASN cc_start: 0.7804 (t0) cc_final: 0.7336 (t0) REVERT: A 343 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: A 370 LEU cc_start: 0.8756 (mt) cc_final: 0.8518 (mm) REVERT: A 375 GLU cc_start: 0.7613 (pt0) cc_final: 0.7068 (pt0) REVERT: A 378 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7874 (ttpt) REVERT: A 385 LYS cc_start: 0.8369 (mmmt) cc_final: 0.8006 (mtpp) REVERT: A 388 SER cc_start: 0.8575 (t) cc_final: 0.8038 (p) REVERT: A 389 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8713 (mttm) REVERT: A 413 GLU cc_start: 0.7321 (tt0) cc_final: 0.7096 (tt0) REVERT: A 416 SER cc_start: 0.8943 (m) cc_final: 0.8460 (p) REVERT: A 427 ILE cc_start: 0.8188 (mt) cc_final: 0.7760 (tt) REVERT: A 433 GLU cc_start: 0.7725 (mp0) cc_final: 0.7128 (mp0) REVERT: A 437 TRP cc_start: 0.8302 (m100) cc_final: 0.7300 (m-10) REVERT: A 440 SER cc_start: 0.8401 (t) cc_final: 0.8102 (t) REVERT: A 453 TYR cc_start: 0.8096 (p90) cc_final: 0.7698 (p90) REVERT: A 465 ASN cc_start: 0.8191 (p0) cc_final: 0.7794 (p0) REVERT: H 13 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7369 (mtmm) REVERT: H 16 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7191 (mt-10) REVERT: H 29 PHE cc_start: 0.8107 (t80) cc_final: 0.7770 (m-80) REVERT: H 81 LYS cc_start: 0.8180 (mttt) cc_final: 0.7941 (mptt) REVERT: H 99 TYR cc_start: 0.7947 (m-80) cc_final: 0.7518 (m-80) REVERT: L 7 SER cc_start: 0.8704 (m) cc_final: 0.8275 (p) REVERT: L 10 SER cc_start: 0.8025 (t) cc_final: 0.7759 (m) REVERT: L 42 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8048 (mmmt) REVERT: L 58 VAL cc_start: 0.8857 (t) cc_final: 0.8546 (p) REVERT: L 103 LYS cc_start: 0.7864 (tttt) cc_final: 0.7379 (tttt) REVERT: M 59 TYR cc_start: 0.8477 (m-80) cc_final: 0.7911 (m-80) REVERT: N 24 ARG cc_start: 0.7136 (ttm170) cc_final: 0.6783 (ttm170) REVERT: N 56 SER cc_start: 0.8641 (t) cc_final: 0.8362 (p) REVERT: N 78 LEU cc_start: 0.8203 (tt) cc_final: 0.7972 (tt) outliers start: 32 outliers final: 28 residues processed: 263 average time/residue: 0.2220 time to fit residues: 75.6469 Evaluate side-chains 278 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 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 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 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 27 GLN 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: 0.9980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 74 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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** ** M 52 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 = 0.3328 r_free = 0.3328 target = 0.105196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092898 restraints weight = 11973.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096103 restraints weight = 5034.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098021 restraints weight = 2558.855| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6783 Z= 0.141 Angle : 0.655 8.926 9226 Z= 0.338 Chirality : 0.047 0.186 997 Planarity : 0.005 0.043 1179 Dihedral : 5.283 39.668 954 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 4.82 % Allowed : 22.87 % Favored : 72.31 % 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: -2.63 (0.27), residues: 841 helix: -2.61 (2.45), residues: 6 sheet: -0.86 (0.29), residues: 340 loop : -2.49 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 7 HIS 0.007 0.001 HIS A 274 PHE 0.028 0.002 PHE A 410 TYR 0.032 0.002 TYR N 49 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 2.65975 ( 3) hydrogen bonds : bond 0.03615 ( 151) hydrogen bonds : angle 5.68590 ( 423) SS BOND : bond 0.00521 ( 13) SS BOND : angle 1.35814 ( 26) covalent geometry : bond 0.00312 ( 6769) covalent geometry : angle 0.64998 ( 9197) *********************** 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 275 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8294 (mttt) cc_final: 0.7927 (mmtt) REVERT: A 128 LYS cc_start: 0.8149 (pttm) cc_final: 0.7877 (pttm) REVERT: A 132 PHE cc_start: 0.7620 (m-80) cc_final: 0.7386 (m-80) REVERT: A 162 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7560 (mt-10) REVERT: A 245 SER cc_start: 0.8504 (t) cc_final: 0.8214 (p) REVERT: A 251 ASP cc_start: 0.7549 (m-30) cc_final: 0.7270 (m-30) REVERT: A 262 ILE cc_start: 0.8573 (mt) cc_final: 0.8320 (tt) REVERT: A 292 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7354 (ptt180) REVERT: A 302 ILE cc_start: 0.8758 (mt) cc_final: 0.8288 (mm) REVERT: A 307 VAL cc_start: 0.8556 (m) cc_final: 0.8251 (t) REVERT: A 309 ASN cc_start: 0.7775 (t0) cc_final: 0.7318 (t0) REVERT: A 343 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: A 370 LEU cc_start: 0.8751 (mt) cc_final: 0.8516 (mm) REVERT: A 375 GLU cc_start: 0.7590 (pt0) cc_final: 0.7041 (pt0) REVERT: A 378 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7867 (ttpt) REVERT: A 385 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8010 (mtpp) REVERT: A 388 SER cc_start: 0.8570 (t) cc_final: 0.8015 (p) REVERT: A 389 LYS cc_start: 0.8924 (mtpp) cc_final: 0.8526 (mttm) REVERT: A 416 SER cc_start: 0.8952 (m) cc_final: 0.8465 (p) REVERT: A 427 ILE cc_start: 0.8179 (mt) cc_final: 0.7792 (tt) REVERT: A 433 GLU cc_start: 0.7728 (mp0) cc_final: 0.7141 (mp0) REVERT: A 437 TRP cc_start: 0.8193 (m100) cc_final: 0.7254 (m-10) REVERT: A 440 SER cc_start: 0.8403 (t) cc_final: 0.8093 (t) REVERT: A 453 TYR cc_start: 0.8090 (p90) cc_final: 0.7709 (p90) REVERT: A 465 ASN cc_start: 0.8220 (p0) cc_final: 0.7906 (p0) REVERT: H 13 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7336 (mtmm) REVERT: H 16 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7145 (mt-10) REVERT: H 29 PHE cc_start: 0.8015 (t80) cc_final: 0.7781 (m-80) REVERT: H 33 PHE cc_start: 0.7664 (m-80) cc_final: 0.7426 (m-10) REVERT: H 99 TYR cc_start: 0.7943 (m-80) cc_final: 0.7591 (m-80) REVERT: L 7 SER cc_start: 0.8697 (m) cc_final: 0.8256 (p) REVERT: L 10 SER cc_start: 0.7991 (t) cc_final: 0.7731 (m) REVERT: L 24 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6904 (mmm160) REVERT: L 42 LYS cc_start: 0.8382 (mmmt) cc_final: 0.8030 (mmmt) REVERT: L 58 VAL cc_start: 0.8842 (t) cc_final: 0.8541 (p) REVERT: L 103 LYS cc_start: 0.7886 (tttt) cc_final: 0.7402 (tttt) REVERT: M 59 TYR cc_start: 0.8482 (m-80) cc_final: 0.7942 (m-80) REVERT: M 100 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7673 (m-80) REVERT: N 24 ARG cc_start: 0.7247 (ttm170) cc_final: 0.6968 (ttm170) REVERT: N 56 SER cc_start: 0.8638 (t) cc_final: 0.8359 (p) outliers start: 35 outliers final: 29 residues processed: 254 average time/residue: 0.1924 time to fit residues: 63.2488 Evaluate side-chains 270 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 252 THR 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 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE 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 100 PHE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 27 GLN 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: 0.1980 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 104 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 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 = 0.3360 r_free = 0.3360 target = 0.107010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095010 restraints weight = 12122.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098113 restraints weight = 5123.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099987 restraints weight = 2601.500| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 6783 Z= 0.110 Angle : 0.631 9.106 9226 Z= 0.324 Chirality : 0.047 0.193 997 Planarity : 0.004 0.040 1179 Dihedral : 5.024 39.975 954 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.55 % Allowed : 23.00 % Favored : 72.45 % 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: -2.42 (0.28), residues: 841 helix: -2.30 (2.62), residues: 6 sheet: -0.69 (0.29), residues: 337 loop : -2.37 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 7 HIS 0.005 0.001 HIS A 274 PHE 0.027 0.001 PHE A 410 TYR 0.030 0.001 TYR N 49 ARG 0.003 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 1) link_NAG-ASN : angle 2.13707 ( 3) hydrogen bonds : bond 0.03165 ( 151) hydrogen bonds : angle 5.48218 ( 423) SS BOND : bond 0.00443 ( 13) SS BOND : angle 1.20067 ( 26) covalent geometry : bond 0.00247 ( 6769) covalent geometry : angle 0.62805 ( 9197) ********************** 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 273 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8207 (mttt) cc_final: 0.7913 (mmtt) REVERT: A 128 LYS cc_start: 0.8126 (pttm) cc_final: 0.7843 (pttm) REVERT: A 132 PHE cc_start: 0.7607 (m-80) cc_final: 0.7363 (m-80) REVERT: A 245 SER cc_start: 0.8451 (t) cc_final: 0.8157 (p) REVERT: A 251 ASP cc_start: 0.7528 (m-30) cc_final: 0.7254 (m-30) REVERT: A 262 ILE cc_start: 0.8561 (mt) cc_final: 0.8296 (tt) REVERT: A 292 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7290 (ptt180) REVERT: A 302 ILE cc_start: 0.8743 (mt) cc_final: 0.8256 (mm) REVERT: A 307 VAL cc_start: 0.8500 (m) cc_final: 0.8127 (t) REVERT: A 309 ASN cc_start: 0.7768 (t0) cc_final: 0.7327 (t0) REVERT: A 343 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: A 370 LEU cc_start: 0.8725 (mt) cc_final: 0.8500 (mm) REVERT: A 375 GLU cc_start: 0.7559 (pt0) cc_final: 0.7007 (pt0) REVERT: A 378 LYS cc_start: 0.8137 (ttpt) cc_final: 0.7866 (ttpt) REVERT: A 385 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7967 (mtpp) REVERT: A 389 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8381 (mttm) REVERT: A 399 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6656 (mt-10) REVERT: A 416 SER cc_start: 0.8955 (m) cc_final: 0.8478 (p) REVERT: A 427 ILE cc_start: 0.8130 (mt) cc_final: 0.7726 (tt) REVERT: A 433 GLU cc_start: 0.7729 (mp0) cc_final: 0.7175 (mp0) REVERT: A 437 TRP cc_start: 0.8170 (m100) cc_final: 0.7292 (m-10) REVERT: A 440 SER cc_start: 0.8356 (t) cc_final: 0.8042 (t) REVERT: A 453 TYR cc_start: 0.8059 (p90) cc_final: 0.7669 (p90) REVERT: A 465 ASN cc_start: 0.8318 (p0) cc_final: 0.8043 (p0) REVERT: H 13 LYS cc_start: 0.7634 (mtmm) cc_final: 0.7245 (mtmm) REVERT: H 16 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6983 (mt-10) REVERT: H 33 PHE cc_start: 0.7703 (m-80) cc_final: 0.7474 (m-10) REVERT: L 7 SER cc_start: 0.8626 (m) cc_final: 0.8212 (p) REVERT: L 10 SER cc_start: 0.7905 (t) cc_final: 0.7659 (m) REVERT: L 24 ARG cc_start: 0.7126 (mmm160) cc_final: 0.6896 (mmm160) REVERT: L 42 LYS cc_start: 0.8311 (mmmt) cc_final: 0.7975 (mmmt) REVERT: L 58 VAL cc_start: 0.8812 (t) cc_final: 0.8530 (p) REVERT: L 103 LYS cc_start: 0.7908 (tttt) cc_final: 0.7404 (tttt) REVERT: M 59 TYR cc_start: 0.8530 (m-80) cc_final: 0.8049 (m-80) REVERT: N 56 SER cc_start: 0.8661 (t) cc_final: 0.8409 (p) outliers start: 33 outliers final: 30 residues processed: 253 average time/residue: 0.1986 time to fit residues: 65.7930 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 : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 252 THR 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 100 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 ILE 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 100 PHE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain N residue 27 GLN 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 95 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: 0.0970 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.0370 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095343 restraints weight = 12085.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.098465 restraints weight = 5125.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100390 restraints weight = 2618.750| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6783 Z= 0.111 Angle : 0.637 8.990 9226 Z= 0.324 Chirality : 0.047 0.196 997 Planarity : 0.004 0.040 1179 Dihedral : 5.004 39.558 954 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.27 % Allowed : 23.97 % 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: -2.31 (0.28), residues: 841 helix: -2.49 (2.40), residues: 6 sheet: -0.65 (0.30), residues: 317 loop : -2.22 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 7 HIS 0.003 0.001 HIS A 274 PHE 0.027 0.001 PHE A 410 TYR 0.031 0.001 TYR N 49 ARG 0.006 0.000 ARG N 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 1) link_NAG-ASN : angle 2.18253 ( 3) hydrogen bonds : bond 0.03186 ( 151) hydrogen bonds : angle 5.40298 ( 423) SS BOND : bond 0.00450 ( 13) SS BOND : angle 1.16011 ( 26) covalent geometry : bond 0.00250 ( 6769) covalent geometry : angle 0.63415 ( 9197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2702.73 seconds wall clock time: 47 minutes 48.90 seconds (2868.90 seconds total)