Starting phenix.real_space_refine on Sat May 10 16:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gau_29908/05_2025/8gau_29908.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gau_29908/05_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_29908/05_2025/8gau_29908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gau_29908/05_2025/8gau_29908.map" model { file = "/net/cci-nas-00/data/ceres_data/8gau_29908/05_2025/8gau_29908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gau_29908/05_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-5687/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: 4.08, per 1000 atoms: 0.62 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: 1.34 Conformation dependent library (CDL) restraints added in 845.9 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: 0.99 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: 1.80 Time building geometry restraints manager: 1.63 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.860 Find NCS groups from input model: 0.070 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- 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 : 0.684 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: 0.1851 time to fit residues: 73.1412 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 : 0.730 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093571 restraints weight = 11678.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096810 restraints weight = 4925.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098769 restraints weight = 2515.499| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 59.023 959 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 : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8274 (mttt) cc_final: 0.7880 (mmtt) REVERT: A 104 ASN cc_start: 0.8331 (m-40) cc_final: 0.7967 (m110) REVERT: A 128 LYS cc_start: 0.8022 (pttm) cc_final: 0.7335 (pttm) REVERT: A 142 ASN cc_start: 0.8025 (t0) cc_final: 0.7768 (t0) REVERT: A 162 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 245 SER cc_start: 0.8514 (t) cc_final: 0.7910 (p) REVERT: A 251 ASP cc_start: 0.7537 (m-30) cc_final: 0.7195 (m-30) REVERT: A 258 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6860 (mt-10) REVERT: A 261 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7575 (tmmm) REVERT: A 276 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6674 (mm-30) REVERT: A 292 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7298 (ptt180) REVERT: A 302 ILE cc_start: 0.8621 (mt) cc_final: 0.8153 (mm) REVERT: A 327 ARG cc_start: 0.8303 (ptt-90) cc_final: 0.8081 (ptt-90) REVERT: A 343 GLU cc_start: 0.7384 (mp0) cc_final: 0.6858 (mp0) REVERT: A 356 ASP cc_start: 0.8238 (t0) cc_final: 0.8027 (t0) REVERT: A 370 LEU cc_start: 0.8703 (mt) cc_final: 0.8376 (mm) REVERT: A 375 GLU cc_start: 0.7655 (pt0) cc_final: 0.7082 (pt0) REVERT: A 378 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7949 (ttpt) REVERT: A 381 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7071 (mm-30) REVERT: A 385 LYS cc_start: 0.8366 (mmmt) cc_final: 0.8024 (mtpp) REVERT: A 388 SER cc_start: 0.8431 (t) cc_final: 0.7982 (p) REVERT: A 389 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8701 (mtpp) REVERT: A 399 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6758 (mt-10) REVERT: A 413 GLU cc_start: 0.7297 (tt0) cc_final: 0.7058 (tt0) REVERT: A 416 SER cc_start: 0.8911 (m) cc_final: 0.8410 (p) REVERT: A 427 ILE cc_start: 0.8193 (mt) cc_final: 0.7791 (tp) REVERT: A 433 GLU cc_start: 0.7660 (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: 0.7685 (p90) REVERT: A 463 ASP cc_start: 0.8005 (t0) cc_final: 0.7796 (t0) REVERT: H 7 TRP cc_start: 0.7571 (p-90) cc_final: 0.7363 (p-90) REVERT: H 13 LYS cc_start: 0.7683 (mtmm) cc_final: 0.7423 (mtmm) REVERT: H 25 TYR cc_start: 0.7917 (m-80) cc_final: 0.7700 (m-10) REVERT: H 31 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6851 (p90) REVERT: H 100 HIS cc_start: 0.7407 (t-90) cc_final: 0.6947 (t-90) REVERT: H 100 LEU cc_start: 0.8087 (mt) cc_final: 0.7418 (mt) REVERT: H 100 TYR cc_start: 0.8065 (m-80) cc_final: 0.7518 (m-80) REVERT: L 4 MET cc_start: 0.5586 (mpp) cc_final: 0.5370 (mpp) REVERT: L 7 SER cc_start: 0.8636 (m) cc_final: 0.8229 (p) REVERT: L 58 VAL cc_start: 0.8801 (t) cc_final: 0.8509 (p) REVERT: L 103 LYS cc_start: 0.7748 (tttt) cc_final: 0.7281 (tttt) REVERT: L 107 LYS cc_start: 0.7782 (pttp) cc_final: 0.7239 (tppt) REVERT: M 32 TYR cc_start: 0.7734 (m-80) cc_final: 0.7444 (m-10) REVERT: M 59 TYR cc_start: 0.8216 (m-10) cc_final: 0.7851 (m-80) REVERT: M 96 SER cc_start: 0.8377 (m) cc_final: 0.7995 (p) REVERT: N 56 SER cc_start: 0.8646 (t) cc_final: 0.8268 (p) REVERT: N 67 TYR cc_start: 0.8319 (t80) cc_final: 0.8063 (t80) REVERT: N 82 ASP cc_start: 0.8192 (m-30) cc_final: 0.7727 (m-30) REVERT: N 86 TYR cc_start: 0.8103 (m-10) cc_final: 0.7453 (m-80) outliers start: 24 outliers final: 15 residues processed: 268 average time/residue: 0.1909 time to fit residues: 66.4203 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 : 0.677 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** M 73 ASN N 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090759 restraints weight = 11832.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093950 restraints weight = 4938.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.095917 restraints weight = 2506.599| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6783 Z= 0.219 Angle : 0.692 8.190 9226 Z= 0.361 Chirality : 0.048 0.151 997 Planarity : 0.006 0.055 1179 Dihedral : 6.197 49.924 958 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 4.41 % Allowed : 15.43 % Favored : 80.17 % 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: -3.41 (0.26), residues: 841 helix: -3.71 (1.31), residues: 6 sheet: -1.47 (0.28), residues: 329 loop : -2.94 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 7 HIS 0.004 0.001 HIS A 264 PHE 0.024 0.002 PHE H 78 TYR 0.028 0.002 TYR N 49 ARG 0.005 0.001 ARG M 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 1) link_NAG-ASN : angle 3.65347 ( 3) hydrogen bonds : bond 0.04689 ( 151) hydrogen bonds : angle 6.19255 ( 423) SS BOND : bond 0.00467 ( 13) SS BOND : angle 1.23547 ( 26) covalent geometry : bond 0.00472 ( 6769) covalent geometry : angle 0.68635 ( 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 285 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8349 (mttt) cc_final: 0.7960 (mmtt) REVERT: A 104 ASN cc_start: 0.8325 (m-40) cc_final: 0.8004 (m-40) REVERT: A 128 LYS cc_start: 0.8015 (pttm) cc_final: 0.7687 (pttm) REVERT: A 245 SER cc_start: 0.8531 (t) cc_final: 0.8014 (p) REVERT: A 251 ASP cc_start: 0.7595 (m-30) cc_final: 0.7279 (m-30) REVERT: A 276 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6706 (mm-30) REVERT: A 292 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7345 (ptt180) REVERT: A 302 ILE cc_start: 0.8703 (mt) cc_final: 0.8211 (mm) REVERT: A 307 VAL cc_start: 0.8669 (m) cc_final: 0.8383 (t) REVERT: A 309 ASN cc_start: 0.7703 (t0) cc_final: 0.7352 (t0) REVERT: A 343 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: A 356 ASP cc_start: 0.8296 (t0) cc_final: 0.8074 (t0) REVERT: A 370 LEU cc_start: 0.8781 (mt) cc_final: 0.8548 (mm) REVERT: A 375 GLU cc_start: 0.7643 (pt0) cc_final: 0.7116 (pt0) REVERT: A 378 LYS cc_start: 0.8266 (ttpt) cc_final: 0.8063 (ttpt) REVERT: A 385 LYS cc_start: 0.8374 (mmmt) cc_final: 0.8028 (mtpp) REVERT: A 388 SER cc_start: 0.8576 (t) cc_final: 0.8045 (p) REVERT: A 389 LYS cc_start: 0.8966 (mtpp) cc_final: 0.8606 (mtpp) REVERT: A 413 GLU cc_start: 0.7333 (tt0) cc_final: 0.7058 (tt0) REVERT: A 427 ILE cc_start: 0.8291 (mt) cc_final: 0.7860 (tt) REVERT: A 433 GLU cc_start: 0.7721 (mp0) cc_final: 0.7065 (mp0) REVERT: A 437 TRP cc_start: 0.8352 (m100) cc_final: 0.7474 (m-10) REVERT: A 440 SER cc_start: 0.8540 (t) cc_final: 0.8305 (t) REVERT: A 453 TYR cc_start: 0.8033 (p90) cc_final: 0.7729 (p90) REVERT: H 7 TRP cc_start: 0.7617 (p-90) cc_final: 0.7304 (p-90) REVERT: H 13 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7509 (mtmm) REVERT: H 21 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7970 (p) REVERT: H 81 LYS cc_start: 0.8170 (mttt) cc_final: 0.7887 (mptt) REVERT: H 99 TYR cc_start: 0.7984 (m-80) cc_final: 0.7487 (m-80) REVERT: H 100 LEU cc_start: 0.8222 (mt) cc_final: 0.7883 (mp) REVERT: L 7 SER cc_start: 0.8663 (m) cc_final: 0.8227 (p) REVERT: L 22 THR cc_start: 0.7797 (p) cc_final: 0.7439 (p) REVERT: L 58 VAL cc_start: 0.8827 (t) cc_final: 0.8522 (p) REVERT: L 103 LYS cc_start: 0.7873 (tttt) cc_final: 0.7337 (tttt) REVERT: M 32 TYR cc_start: 0.7872 (m-80) cc_final: 0.7525 (m-10) REVERT: M 96 SER cc_start: 0.8264 (m) cc_final: 0.7927 (p) REVERT: N 24 ARG cc_start: 0.7160 (ttm170) cc_final: 0.6956 (ttm170) REVERT: N 56 SER cc_start: 0.8660 (t) cc_final: 0.8304 (p) REVERT: N 67 TYR cc_start: 0.8358 (t80) cc_final: 0.8136 (t80) REVERT: N 82 ASP cc_start: 0.8221 (m-30) cc_final: 0.7997 (m-30) REVERT: N 86 TYR cc_start: 0.8033 (m-10) cc_final: 0.7464 (m-80) outliers start: 32 outliers final: 24 residues processed: 266 average time/residue: 0.1880 time to fit residues: 64.6541 Evaluate side-chains 268 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 398 VAL 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 60 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 82 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: 7.9990 chunk 43 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.092984 restraints weight = 11907.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096198 restraints weight = 4958.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098177 restraints weight = 2513.212| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3052 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= 0.129 Angle : 0.617 8.789 9226 Z= 0.319 Chirality : 0.046 0.164 997 Planarity : 0.004 0.049 1179 Dihedral : 5.459 45.688 954 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.68 % Allowed : 16.53 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.27), residues: 841 helix: -2.87 (2.05), residues: 6 sheet: -1.16 (0.29), residues: 344 loop : -2.69 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 7 HIS 0.002 0.001 HIS A 184 PHE 0.018 0.001 PHE H 78 TYR 0.030 0.002 TYR N 49 ARG 0.004 0.000 ARG A 292 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 1) link_NAG-ASN : angle 2.72634 ( 3) hydrogen bonds : bond 0.03594 ( 151) hydrogen bonds : angle 5.75594 ( 423) SS BOND : bond 0.00382 ( 13) SS BOND : angle 1.01910 ( 26) covalent geometry : bond 0.00279 ( 6769) covalent geometry : angle 0.61390 ( 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 281 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.762 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: 0.8296 (mttt) cc_final: 0.7943 (mmtt) REVERT: A 104 ASN cc_start: 0.8272 (m-40) cc_final: 0.8046 (m-40) REVERT: A 128 LYS cc_start: 0.8043 (pttm) cc_final: 0.7777 (pttm) REVERT: A 245 SER cc_start: 0.8496 (t) cc_final: 0.8094 (p) REVERT: A 249 LYS cc_start: 0.8397 (mttt) cc_final: 0.7468 (mtpp) REVERT: A 251 ASP cc_start: 0.7638 (m-30) cc_final: 0.7342 (m-30) REVERT: A 271 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8584 (p) REVERT: A 276 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6670 (mm-30) REVERT: A 292 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7285 (ptt180) REVERT: A 302 ILE cc_start: 0.8654 (mt) cc_final: 0.8152 (mm) REVERT: A 306 ASN cc_start: 0.7899 (t0) cc_final: 0.7587 (t0) REVERT: A 307 VAL cc_start: 0.8609 (m) cc_final: 0.8167 (t) REVERT: A 309 ASN cc_start: 0.7776 (t0) cc_final: 0.7378 (t0) REVERT: A 316 TYR cc_start: 0.7996 (m-10) cc_final: 0.7651 (m-10) REVERT: A 343 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: A 356 ASP cc_start: 0.8219 (t0) cc_final: 0.7960 (t0) REVERT: A 370 LEU cc_start: 0.8761 (mt) cc_final: 0.8531 (mm) REVERT: A 375 GLU cc_start: 0.7558 (pt0) cc_final: 0.7119 (pt0) REVERT: A 378 LYS cc_start: 0.8294 (ttpt) cc_final: 0.8084 (ttpt) REVERT: A 385 LYS cc_start: 0.8460 (mmmt) cc_final: 0.8067 (mtpp) REVERT: A 388 SER cc_start: 0.8620 (t) cc_final: 0.8080 (p) REVERT: A 389 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8449 (mttp) REVERT: A 403 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7633 (mtp180) REVERT: A 413 GLU cc_start: 0.7279 (tt0) cc_final: 0.6997 (tt0) REVERT: A 416 SER cc_start: 0.8943 (m) cc_final: 0.8424 (p) REVERT: A 427 ILE cc_start: 0.8227 (mt) cc_final: 0.7960 (tt) REVERT: A 433 GLU cc_start: 0.7783 (mp0) cc_final: 0.7019 (mp0) REVERT: A 437 TRP cc_start: 0.8329 (m100) cc_final: 0.7512 (m-10) REVERT: A 440 SER cc_start: 0.8487 (t) cc_final: 0.8245 (t) REVERT: A 453 TYR cc_start: 0.8061 (p90) cc_final: 0.7721 (p90) REVERT: H 7 TRP cc_start: 0.7495 (p-90) cc_final: 0.7229 (p-90) REVERT: H 13 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7347 (mtmm) REVERT: H 16 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7182 (mt-10) REVERT: H 99 TYR cc_start: 0.7899 (m-80) cc_final: 0.7546 (m-80) REVERT: H 100 LEU cc_start: 0.8055 (mt) cc_final: 0.7752 (mp) REVERT: L 7 SER cc_start: 0.8686 (m) cc_final: 0.8244 (p) REVERT: L 58 VAL cc_start: 0.8820 (t) cc_final: 0.8536 (p) REVERT: L 103 LYS cc_start: 0.7822 (tttt) cc_final: 0.7254 (tttt) REVERT: M 32 TYR cc_start: 0.7677 (m-80) cc_final: 0.7446 (m-10) REVERT: M 59 TYR cc_start: 0.8473 (m-80) cc_final: 0.8071 (m-80) REVERT: M 83 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8166 (ttmm) REVERT: M 96 SER cc_start: 0.8223 (m) cc_final: 0.7971 (p) REVERT: M 100 TYR cc_start: 0.7747 (t80) cc_final: 0.7491 (t80) REVERT: N 56 SER cc_start: 0.8625 (t) cc_final: 0.8321 (p) REVERT: N 67 TYR cc_start: 0.8374 (t80) cc_final: 0.7999 (t80) outliers start: 34 outliers final: 25 residues processed: 261 average time/residue: 0.1919 time to fit residues: 65.3161 Evaluate side-chains 273 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 18 LEU 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 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.105908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093408 restraints weight = 11781.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096579 restraints weight = 4917.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098546 restraints weight = 2489.799| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6783 Z= 0.118 Angle : 0.603 8.137 9226 Z= 0.310 Chirality : 0.046 0.165 997 Planarity : 0.004 0.049 1179 Dihedral : 5.220 43.419 954 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.41 % Allowed : 18.18 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.27), residues: 841 helix: -2.73 (2.12), residues: 6 sheet: -0.86 (0.29), residues: 341 loop : -2.65 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 7 HIS 0.002 0.001 HIS N 90 PHE 0.017 0.001 PHE H 78 TYR 0.030 0.001 TYR N 49 ARG 0.005 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 1) link_NAG-ASN : angle 2.63946 ( 3) hydrogen bonds : bond 0.03427 ( 151) hydrogen bonds : angle 5.53314 ( 423) SS BOND : bond 0.00310 ( 13) SS BOND : angle 0.92701 ( 26) covalent geometry : bond 0.00257 ( 6769) covalent geometry : angle 0.59988 ( 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 279 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 0.751 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: 0.8286 (mttt) cc_final: 0.7904 (mmtt) REVERT: A 104 ASN cc_start: 0.8303 (m-40) cc_final: 0.8001 (m-40) REVERT: A 128 LYS cc_start: 0.8015 (pttm) cc_final: 0.7744 (pttm) REVERT: A 245 SER cc_start: 0.8468 (t) cc_final: 0.8125 (p) REVERT: A 251 ASP cc_start: 0.7687 (m-30) cc_final: 0.7427 (m-30) REVERT: A 276 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6667 (mm-30) REVERT: A 292 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7241 (ptt180) REVERT: A 302 ILE cc_start: 0.8659 (mt) cc_final: 0.8144 (mm) REVERT: A 307 VAL cc_start: 0.8579 (m) cc_final: 0.8268 (t) REVERT: A 309 ASN cc_start: 0.7843 (t0) cc_final: 0.7368 (t0) REVERT: A 316 TYR cc_start: 0.7958 (m-10) cc_final: 0.7602 (m-10) REVERT: A 327 ARG cc_start: 0.8325 (ptt-90) cc_final: 0.8092 (ptt-90) REVERT: A 343 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: A 356 ASP cc_start: 0.8191 (t0) cc_final: 0.7966 (t0) REVERT: A 370 LEU cc_start: 0.8704 (mt) cc_final: 0.8386 (mm) REVERT: A 375 GLU cc_start: 0.7573 (pt0) cc_final: 0.7109 (pt0) REVERT: A 378 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7993 (ttpt) REVERT: A 385 LYS cc_start: 0.8335 (mmmt) cc_final: 0.7976 (mtpp) REVERT: A 388 SER cc_start: 0.8586 (t) cc_final: 0.8051 (p) REVERT: A 389 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8470 (mttm) REVERT: A 399 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6722 (mt-10) REVERT: A 403 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7461 (mtm180) REVERT: A 413 GLU cc_start: 0.7302 (tt0) cc_final: 0.7011 (tt0) REVERT: A 416 SER cc_start: 0.8948 (m) cc_final: 0.8485 (p) REVERT: A 427 ILE cc_start: 0.8185 (mt) cc_final: 0.7280 (tt) REVERT: A 433 GLU cc_start: 0.7722 (mp0) cc_final: 0.7213 (mp0) REVERT: A 437 TRP cc_start: 0.8317 (m100) cc_final: 0.7482 (m-10) REVERT: A 440 SER cc_start: 0.8463 (t) cc_final: 0.8165 (t) REVERT: A 453 TYR cc_start: 0.8057 (p90) cc_final: 0.7668 (p90) REVERT: H 7 TRP cc_start: 0.7517 (p-90) cc_final: 0.7273 (p-90) REVERT: H 13 LYS cc_start: 0.7632 (mtmm) cc_final: 0.7302 (mtmm) REVERT: H 16 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7159 (mt-10) REVERT: H 39 GLN cc_start: 0.8039 (tt0) cc_final: 0.7796 (tm-30) REVERT: H 99 TYR cc_start: 0.7931 (m-80) cc_final: 0.7560 (m-80) REVERT: H 100 LEU cc_start: 0.7989 (mt) cc_final: 0.7704 (mp) REVERT: L 7 SER cc_start: 0.8646 (m) cc_final: 0.8227 (p) REVERT: L 58 VAL cc_start: 0.8816 (t) cc_final: 0.8505 (p) REVERT: L 103 LYS cc_start: 0.7832 (tttt) cc_final: 0.7278 (tttt) REVERT: M 32 TYR cc_start: 0.7672 (m-80) cc_final: 0.7443 (m-10) REVERT: M 59 TYR cc_start: 0.8507 (m-80) cc_final: 0.8023 (m-80) REVERT: M 83 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8175 (ttmm) REVERT: M 96 SER cc_start: 0.8337 (m) cc_final: 0.8037 (p) REVERT: M 100 TYR cc_start: 0.7788 (t80) cc_final: 0.7489 (t80) REVERT: N 56 SER cc_start: 0.8653 (t) cc_final: 0.8379 (p) REVERT: N 89 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7183 (tt0) outliers start: 32 outliers final: 24 residues processed: 258 average time/residue: 0.1929 time to fit residues: 64.4263 Evaluate side-chains 268 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 19 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain 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 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 0.0570 chunk 71 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093651 restraints weight = 11750.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.096831 restraints weight = 4906.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098796 restraints weight = 2490.661| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3572 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= 0.101 Angle : 0.581 8.133 9226 Z= 0.297 Chirality : 0.045 0.168 997 Planarity : 0.004 0.046 1179 Dihedral : 4.978 43.769 954 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.86 % Allowed : 19.28 % 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: -2.55 (0.28), residues: 841 helix: -2.50 (2.35), residues: 6 sheet: -0.72 (0.30), residues: 324 loop : -2.47 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 7 HIS 0.002 0.001 HIS A 184 PHE 0.016 0.001 PHE H 78 TYR 0.029 0.001 TYR N 49 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 1) link_NAG-ASN : angle 2.20099 ( 3) hydrogen bonds : bond 0.03061 ( 151) hydrogen bonds : angle 5.31014 ( 423) SS BOND : bond 0.00278 ( 13) SS BOND : angle 0.82633 ( 26) covalent geometry : bond 0.00224 ( 6769) covalent geometry : angle 0.57882 ( 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 273 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8273 (mttt) cc_final: 0.7880 (mmtt) REVERT: A 104 ASN cc_start: 0.8349 (m-40) cc_final: 0.8136 (m110) REVERT: A 128 LYS cc_start: 0.8013 (pttm) cc_final: 0.7758 (pttm) REVERT: A 245 SER cc_start: 0.8471 (t) cc_final: 0.8163 (p) REVERT: A 249 LYS cc_start: 0.8407 (mttt) cc_final: 0.7553 (mtpp) REVERT: A 251 ASP cc_start: 0.7691 (m-30) cc_final: 0.7453 (m-30) REVERT: A 292 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7280 (ptt180) REVERT: A 302 ILE cc_start: 0.8661 (mt) cc_final: 0.8154 (mm) REVERT: A 307 VAL cc_start: 0.8482 (m) cc_final: 0.8150 (t) REVERT: A 309 ASN cc_start: 0.7828 (t0) cc_final: 0.7384 (t0) REVERT: A 316 TYR cc_start: 0.7925 (m-10) cc_final: 0.7677 (m-10) REVERT: A 327 ARG cc_start: 0.8339 (ptt-90) cc_final: 0.8118 (ptt-90) REVERT: A 343 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 370 LEU cc_start: 0.8706 (mt) cc_final: 0.8377 (mm) REVERT: A 375 GLU cc_start: 0.7571 (pt0) cc_final: 0.7131 (pt0) REVERT: A 378 LYS cc_start: 0.8279 (ttpt) cc_final: 0.7987 (ttpt) REVERT: A 385 LYS cc_start: 0.8316 (mmmt) cc_final: 0.7983 (mtpp) REVERT: A 388 SER cc_start: 0.8608 (t) cc_final: 0.8084 (p) REVERT: A 399 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6644 (mt-10) REVERT: A 413 GLU cc_start: 0.7326 (tt0) cc_final: 0.7051 (tt0) REVERT: A 416 SER cc_start: 0.8939 (m) cc_final: 0.8467 (p) REVERT: A 427 ILE cc_start: 0.8135 (mt) cc_final: 0.7876 (tt) REVERT: A 433 GLU cc_start: 0.7723 (mp0) cc_final: 0.7044 (mp0) REVERT: A 437 TRP cc_start: 0.8284 (m100) cc_final: 0.7454 (m-10) REVERT: A 440 SER cc_start: 0.8367 (t) cc_final: 0.8076 (t) REVERT: A 453 TYR cc_start: 0.8057 (p90) cc_final: 0.7647 (p90) REVERT: H 16 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7041 (mt-10) REVERT: H 29 PHE cc_start: 0.8090 (t80) cc_final: 0.7881 (m-80) REVERT: H 39 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: H 59 TYR cc_start: 0.7631 (m-10) cc_final: 0.7408 (m-10) REVERT: H 100 LEU cc_start: 0.7929 (mt) cc_final: 0.7727 (mt) REVERT: L 7 SER cc_start: 0.8598 (m) cc_final: 0.8173 (p) REVERT: L 10 SER cc_start: 0.7990 (t) cc_final: 0.7734 (m) REVERT: L 42 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8163 (mmmt) REVERT: L 58 VAL cc_start: 0.8760 (t) cc_final: 0.8447 (p) REVERT: L 103 LYS cc_start: 0.7805 (tttt) cc_final: 0.7365 (tttt) REVERT: M 59 TYR cc_start: 0.8555 (m-80) cc_final: 0.8021 (m-80) REVERT: M 96 SER cc_start: 0.8305 (m) cc_final: 0.8030 (p) REVERT: M 100 TYR cc_start: 0.7787 (t80) cc_final: 0.7487 (t80) REVERT: N 56 SER cc_start: 0.8686 (t) cc_final: 0.8421 (p) REVERT: N 89 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7208 (tt0) outliers start: 28 outliers final: 21 residues processed: 253 average time/residue: 0.1815 time to fit residues: 60.0355 Evaluate side-chains 262 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS 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 17 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 39 GLN 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 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: 3.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.088642 restraints weight = 12021.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.091751 restraints weight = 5025.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.093634 restraints weight = 2558.017| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 6783 Z= 0.369 Angle : 0.804 10.001 9226 Z= 0.421 Chirality : 0.052 0.174 997 Planarity : 0.006 0.070 1179 Dihedral : 6.068 36.930 954 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 4.82 % Allowed : 20.52 % Favored : 74.66 % 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: -3.12 (0.26), residues: 841 helix: -2.79 (2.40), residues: 6 sheet: -1.23 (0.28), residues: 349 loop : -2.82 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 7 HIS 0.008 0.002 HIS N 90 PHE 0.038 0.003 PHE H 78 TYR 0.038 0.003 TYR N 49 ARG 0.007 0.001 ARG M 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 1) link_NAG-ASN : angle 4.11368 ( 3) hydrogen bonds : bond 0.05252 ( 151) hydrogen bonds : angle 6.21716 ( 423) SS BOND : bond 0.00611 ( 13) SS BOND : angle 1.53819 ( 26) covalent geometry : bond 0.00795 ( 6769) covalent geometry : angle 0.79774 ( 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 300 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8297 (mttt) cc_final: 0.7943 (mmtt) REVERT: A 128 LYS cc_start: 0.8111 (pttm) cc_final: 0.7779 (pttm) REVERT: A 251 ASP cc_start: 0.7626 (m-30) cc_final: 0.7311 (m-30) REVERT: A 252 THR cc_start: 0.8643 (m) cc_final: 0.8422 (t) REVERT: A 276 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6727 (mm-30) REVERT: A 292 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.6881 (ppp80) REVERT: A 302 ILE cc_start: 0.8746 (mt) cc_final: 0.8310 (mm) REVERT: A 306 ASN cc_start: 0.8013 (t0) cc_final: 0.7751 (t0) REVERT: A 307 VAL cc_start: 0.8659 (m) cc_final: 0.8297 (t) REVERT: A 309 ASN cc_start: 0.7771 (t0) cc_final: 0.7342 (t0) REVERT: A 343 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 375 GLU cc_start: 0.7539 (pt0) cc_final: 0.7127 (pt0) REVERT: A 378 LYS cc_start: 0.8296 (ttpt) cc_final: 0.8066 (ttpt) REVERT: A 385 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8050 (mtpp) REVERT: A 388 SER cc_start: 0.8500 (t) cc_final: 0.7910 (p) REVERT: A 389 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8465 (mttt) REVERT: A 399 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6744 (mt-10) REVERT: A 413 GLU cc_start: 0.7338 (tt0) cc_final: 0.7105 (tt0) REVERT: A 416 SER cc_start: 0.8953 (m) cc_final: 0.8484 (p) REVERT: A 419 ASN cc_start: 0.8115 (t0) cc_final: 0.7840 (t0) REVERT: A 427 ILE cc_start: 0.8405 (mt) cc_final: 0.7993 (tt) REVERT: A 433 GLU cc_start: 0.7735 (mp0) cc_final: 0.7067 (mp0) REVERT: A 437 TRP cc_start: 0.8355 (m100) cc_final: 0.7338 (m-10) REVERT: A 440 SER cc_start: 0.8603 (t) cc_final: 0.8328 (t) REVERT: A 453 TYR cc_start: 0.8100 (p90) cc_final: 0.7719 (p90) REVERT: H 13 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7471 (mtmm) REVERT: H 16 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7464 (mt-10) REVERT: H 22 CYS cc_start: 0.6104 (t) cc_final: 0.5902 (t) REVERT: H 50 GLU cc_start: 0.7279 (pt0) cc_final: 0.7045 (pt0) REVERT: H 81 LYS cc_start: 0.8111 (mttt) cc_final: 0.7864 (mptt) REVERT: H 100 LEU cc_start: 0.8128 (mt) cc_final: 0.7894 (mp) REVERT: L 7 SER cc_start: 0.8813 (m) cc_final: 0.8346 (p) REVERT: L 10 SER cc_start: 0.8216 (t) cc_final: 0.7883 (m) REVERT: L 22 THR cc_start: 0.7850 (p) cc_final: 0.7507 (p) REVERT: L 42 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8157 (mmmt) REVERT: L 103 LYS cc_start: 0.7987 (tttt) cc_final: 0.7504 (tttt) REVERT: M 100 TYR cc_start: 0.7875 (t80) cc_final: 0.7645 (t80) REVERT: N 9 SER cc_start: 0.8724 (m) cc_final: 0.8409 (t) REVERT: N 56 SER cc_start: 0.8595 (t) cc_final: 0.8292 (p) REVERT: N 67 TYR cc_start: 0.8471 (t80) cc_final: 0.8058 (t80) REVERT: N 89 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7331 (tt0) outliers start: 35 outliers final: 27 residues processed: 276 average time/residue: 0.2057 time to fit residues: 73.1605 Evaluate side-chains 284 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 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 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: 0.8980 chunk 31 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.092856 restraints weight = 11850.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.096037 restraints weight = 4961.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097991 restraints weight = 2520.269| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6783 Z= 0.141 Angle : 0.667 8.928 9226 Z= 0.342 Chirality : 0.048 0.182 997 Planarity : 0.005 0.049 1179 Dihedral : 5.456 39.665 954 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.44 % Allowed : 22.87 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.27), residues: 841 helix: -2.36 (2.70), residues: 6 sheet: -1.05 (0.29), residues: 340 loop : -2.55 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 7 HIS 0.003 0.001 HIS A 264 PHE 0.022 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 0.00160 ( 1) link_NAG-ASN : angle 2.74808 ( 3) hydrogen bonds : bond 0.03653 ( 151) hydrogen bonds : angle 5.78762 ( 423) SS BOND : bond 0.00517 ( 13) SS BOND : angle 1.41226 ( 26) covalent geometry : bond 0.00309 ( 6769) covalent geometry : angle 0.66217 ( 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: 25 poor density : 257 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8286 (mttt) cc_final: 0.7864 (mmtt) REVERT: A 128 LYS cc_start: 0.8120 (pttm) cc_final: 0.7834 (pttm) REVERT: A 132 PHE cc_start: 0.7679 (m-80) cc_final: 0.7399 (m-80) REVERT: A 251 ASP cc_start: 0.7655 (m-30) cc_final: 0.7313 (m-30) REVERT: A 252 THR cc_start: 0.8585 (m) cc_final: 0.8363 (t) REVERT: A 262 ILE cc_start: 0.8549 (mt) cc_final: 0.8291 (tt) REVERT: A 292 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7298 (ptt180) REVERT: A 302 ILE cc_start: 0.8773 (mt) cc_final: 0.8287 (mm) REVERT: A 307 VAL cc_start: 0.8556 (m) cc_final: 0.8268 (t) REVERT: A 309 ASN cc_start: 0.7801 (t0) cc_final: 0.7349 (t0) REVERT: A 343 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: A 370 LEU cc_start: 0.8690 (mt) cc_final: 0.8482 (mm) REVERT: A 375 GLU cc_start: 0.7563 (pt0) cc_final: 0.7056 (pt0) REVERT: A 378 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7916 (ttpt) REVERT: A 385 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8001 (mtpp) REVERT: A 388 SER cc_start: 0.8576 (t) cc_final: 0.8034 (p) REVERT: A 389 LYS cc_start: 0.8945 (mtpp) cc_final: 0.8735 (mttm) REVERT: A 413 GLU cc_start: 0.7305 (tt0) cc_final: 0.7089 (tt0) REVERT: A 416 SER cc_start: 0.8939 (m) cc_final: 0.8469 (p) REVERT: A 427 ILE cc_start: 0.8267 (mt) cc_final: 0.7865 (tt) REVERT: A 433 GLU cc_start: 0.7698 (mp0) cc_final: 0.7076 (mp0) REVERT: A 437 TRP cc_start: 0.8287 (m100) cc_final: 0.7306 (m-10) REVERT: A 440 SER cc_start: 0.8469 (t) cc_final: 0.8179 (t) REVERT: A 453 TYR cc_start: 0.8104 (p90) cc_final: 0.7688 (p90) REVERT: A 465 ASN cc_start: 0.8140 (p0) cc_final: 0.7917 (p0) REVERT: H 13 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7391 (mtmm) REVERT: H 16 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7236 (mt-10) REVERT: H 29 PHE cc_start: 0.8083 (t80) cc_final: 0.7764 (m-80) REVERT: H 81 LYS cc_start: 0.8313 (mttt) cc_final: 0.8062 (mptt) REVERT: H 99 TYR cc_start: 0.7854 (m-80) cc_final: 0.7415 (m-80) REVERT: L 7 SER cc_start: 0.8710 (m) cc_final: 0.8260 (p) REVERT: L 42 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8069 (mmmt) REVERT: L 61 ARG cc_start: 0.7867 (ptt180) cc_final: 0.7633 (ptp90) REVERT: L 103 LYS cc_start: 0.7858 (tttt) cc_final: 0.7264 (tttt) REVERT: M 59 TYR cc_start: 0.8455 (m-80) cc_final: 0.7905 (m-80) REVERT: M 96 SER cc_start: 0.8327 (m) cc_final: 0.8076 (p) REVERT: M 100 TYR cc_start: 0.7770 (t80) cc_final: 0.7551 (t80) REVERT: N 24 ARG cc_start: 0.7339 (ttm170) cc_final: 0.7090 (ttm170) REVERT: N 56 SER cc_start: 0.8633 (t) cc_final: 0.8336 (p) REVERT: N 78 LEU cc_start: 0.8226 (tt) cc_final: 0.8005 (tt) outliers start: 25 outliers final: 22 residues processed: 267 average time/residue: 0.2000 time to fit residues: 69.0047 Evaluate side-chains 273 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 249 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS 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 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 100 PHE 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: 2.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.091714 restraints weight = 11964.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094897 restraints weight = 5026.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096830 restraints weight = 2563.311| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 6783 Z= 0.170 Angle : 0.718 12.462 9226 Z= 0.367 Chirality : 0.049 0.264 997 Planarity : 0.005 0.047 1179 Dihedral : 5.456 40.086 954 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 3.86 % Allowed : 23.55 % Favored : 72.59 % 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: -2.65 (0.27), residues: 841 helix: -2.41 (2.63), residues: 6 sheet: -0.84 (0.29), residues: 338 loop : -2.53 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP H 7 HIS 0.005 0.001 HIS A 274 PHE 0.027 0.002 PHE A 410 TYR 0.032 0.002 TYR N 49 ARG 0.005 0.000 ARG A 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 1) link_NAG-ASN : angle 2.88620 ( 3) hydrogen bonds : bond 0.03910 ( 151) hydrogen bonds : angle 5.83356 ( 423) SS BOND : bond 0.00876 ( 13) SS BOND : angle 2.89589 ( 26) covalent geometry : bond 0.00399 ( 6769) covalent geometry : angle 0.70027 ( 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 274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 246 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8283 (mttt) cc_final: 0.7930 (mmtt) REVERT: A 128 LYS cc_start: 0.8136 (pttm) cc_final: 0.7886 (pttm) REVERT: A 132 PHE cc_start: 0.7655 (m-80) cc_final: 0.7397 (m-80) REVERT: A 162 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 245 SER cc_start: 0.8528 (t) cc_final: 0.8105 (p) REVERT: A 251 ASP cc_start: 0.7625 (m-30) cc_final: 0.7295 (m-30) REVERT: A 262 ILE cc_start: 0.8574 (mt) cc_final: 0.8350 (tt) REVERT: A 292 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7188 (ptt180) REVERT: A 302 ILE cc_start: 0.8757 (mt) cc_final: 0.8288 (mm) REVERT: A 307 VAL cc_start: 0.8542 (m) cc_final: 0.8263 (t) REVERT: A 309 ASN cc_start: 0.7769 (t0) cc_final: 0.7326 (t0) REVERT: A 343 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: A 370 LEU cc_start: 0.8719 (mt) cc_final: 0.8501 (mm) REVERT: A 375 GLU cc_start: 0.7568 (pt0) cc_final: 0.7058 (pt0) REVERT: A 378 LYS cc_start: 0.8199 (ttpt) cc_final: 0.7907 (ttpt) REVERT: A 385 LYS cc_start: 0.8373 (mmmt) cc_final: 0.8014 (mtpp) REVERT: A 388 SER cc_start: 0.8573 (t) cc_final: 0.8022 (p) REVERT: A 389 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8719 (mttm) REVERT: A 413 GLU cc_start: 0.7308 (tt0) cc_final: 0.7076 (tt0) REVERT: A 416 SER cc_start: 0.8946 (m) cc_final: 0.8436 (p) REVERT: A 427 ILE cc_start: 0.8296 (mt) cc_final: 0.7897 (tt) REVERT: A 433 GLU cc_start: 0.7641 (mp0) cc_final: 0.7017 (mp0) REVERT: A 437 TRP cc_start: 0.8299 (m100) cc_final: 0.7296 (m-10) REVERT: A 440 SER cc_start: 0.8461 (t) cc_final: 0.8151 (t) REVERT: A 453 TYR cc_start: 0.8093 (p90) cc_final: 0.7700 (p90) REVERT: H 13 LYS cc_start: 0.7775 (mtmm) cc_final: 0.7369 (mtmm) REVERT: H 16 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7190 (mt-10) REVERT: H 29 PHE cc_start: 0.8053 (t80) cc_final: 0.7723 (m-80) REVERT: H 33 PHE cc_start: 0.7710 (m-80) cc_final: 0.7497 (m-10) REVERT: H 99 TYR cc_start: 0.7881 (m-80) cc_final: 0.7395 (m-80) REVERT: L 7 SER cc_start: 0.8687 (m) cc_final: 0.8267 (p) REVERT: L 42 LYS cc_start: 0.8368 (mmmt) cc_final: 0.8033 (mmmt) REVERT: L 58 VAL cc_start: 0.8979 (m) cc_final: 0.8743 (p) REVERT: L 103 LYS cc_start: 0.7891 (tttt) cc_final: 0.7303 (tttt) REVERT: M 40 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.8024 (p) REVERT: M 59 TYR cc_start: 0.8487 (m-80) cc_final: 0.7922 (m-80) REVERT: M 96 SER cc_start: 0.8333 (m) cc_final: 0.8072 (p) REVERT: M 100 TYR cc_start: 0.7793 (t80) cc_final: 0.7565 (t80) REVERT: N 56 SER cc_start: 0.8632 (t) cc_final: 0.8346 (p) outliers start: 28 outliers final: 23 residues processed: 258 average time/residue: 0.1934 time to fit residues: 64.6319 Evaluate side-chains 270 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 100 PHE 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: 0.9980 chunk 42 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 274 HIS 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** N 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.092286 restraints weight = 12116.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095536 restraints weight = 5071.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097496 restraints weight = 2580.682| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 6783 Z= 0.153 Angle : 0.713 12.548 9226 Z= 0.363 Chirality : 0.049 0.246 997 Planarity : 0.005 0.046 1179 Dihedral : 5.308 39.900 954 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.99 % Allowed : 24.66 % Favored : 71.35 % 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: -2.59 (2.46), residues: 6 sheet: -0.93 (0.29), residues: 326 loop : -2.41 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 7 HIS 0.008 0.001 HIS A 274 PHE 0.027 0.002 PHE A 410 TYR 0.032 0.002 TYR N 49 ARG 0.003 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00165 ( 1) link_NAG-ASN : angle 2.56034 ( 3) hydrogen bonds : bond 0.03673 ( 151) hydrogen bonds : angle 5.77340 ( 423) SS BOND : bond 0.00854 ( 13) SS BOND : angle 2.87015 ( 26) covalent geometry : bond 0.00366 ( 6769) covalent geometry : angle 0.69574 ( 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 271 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8295 (mttt) cc_final: 0.7865 (mmtt) REVERT: A 104 ASN cc_start: 0.8258 (m110) cc_final: 0.8036 (m-40) REVERT: A 128 LYS cc_start: 0.8124 (pttm) cc_final: 0.7855 (pttm) REVERT: A 162 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7545 (mt-10) REVERT: A 245 SER cc_start: 0.8524 (t) cc_final: 0.8224 (p) REVERT: A 251 ASP cc_start: 0.7503 (m-30) cc_final: 0.7226 (m-30) REVERT: A 262 ILE cc_start: 0.8595 (mt) cc_final: 0.8364 (tt) REVERT: A 292 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7159 (ptt180) REVERT: A 302 ILE cc_start: 0.8751 (mt) cc_final: 0.8271 (mm) REVERT: A 307 VAL cc_start: 0.8525 (m) cc_final: 0.8229 (t) REVERT: A 309 ASN cc_start: 0.7769 (t0) cc_final: 0.7326 (t0) REVERT: A 343 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6798 (mp0) REVERT: A 370 LEU cc_start: 0.8730 (mt) cc_final: 0.8488 (mm) REVERT: A 375 GLU cc_start: 0.7595 (pt0) cc_final: 0.7054 (pt0) REVERT: A 378 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7879 (ttpt) REVERT: A 385 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8017 (mtpp) REVERT: A 388 SER cc_start: 0.8543 (t) cc_final: 0.7984 (p) REVERT: A 389 LYS cc_start: 0.8922 (mtpp) cc_final: 0.8531 (mttm) REVERT: A 403 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7543 (mtm180) REVERT: A 413 GLU cc_start: 0.7309 (tt0) cc_final: 0.7082 (tt0) REVERT: A 416 SER cc_start: 0.8949 (m) cc_final: 0.8479 (p) REVERT: A 427 ILE cc_start: 0.8259 (mt) cc_final: 0.7355 (tt) REVERT: A 433 GLU cc_start: 0.7715 (mp0) cc_final: 0.7230 (mp0) REVERT: A 437 TRP cc_start: 0.8290 (m100) cc_final: 0.7368 (m-10) REVERT: A 440 SER cc_start: 0.8423 (t) cc_final: 0.8086 (t) REVERT: A 453 TYR cc_start: 0.8075 (p90) cc_final: 0.7650 (p90) REVERT: H 13 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7339 (mtmm) REVERT: H 16 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7104 (mt-10) REVERT: H 29 PHE cc_start: 0.7990 (t80) cc_final: 0.7736 (m-80) REVERT: H 59 TYR cc_start: 0.7483 (m-10) cc_final: 0.7258 (m-10) REVERT: H 99 TYR cc_start: 0.7900 (m-80) cc_final: 0.7410 (m-80) REVERT: L 7 SER cc_start: 0.8682 (m) cc_final: 0.8241 (p) REVERT: L 24 ARG cc_start: 0.7191 (mmm160) cc_final: 0.6984 (mmm160) REVERT: L 42 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8049 (mmmt) REVERT: L 103 LYS cc_start: 0.7877 (tttt) cc_final: 0.7283 (tttt) REVERT: M 40 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7977 (p) REVERT: M 59 TYR cc_start: 0.8492 (m-80) cc_final: 0.7940 (m-80) REVERT: M 96 SER cc_start: 0.8314 (m) cc_final: 0.8090 (p) REVERT: M 100 TYR cc_start: 0.7755 (t80) cc_final: 0.7511 (t80) REVERT: N 56 SER cc_start: 0.8646 (t) cc_final: 0.8366 (p) outliers start: 29 outliers final: 25 residues processed: 254 average time/residue: 0.1996 time to fit residues: 65.5407 Evaluate side-chains 265 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS 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 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER 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 40 VAL Chi-restraints excluded: chain M residue 100 PHE 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 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 0.0040 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.107396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095341 restraints weight = 12048.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098471 restraints weight = 5088.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100312 restraints weight = 2590.831| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 6783 Z= 0.124 Angle : 0.688 11.908 9226 Z= 0.348 Chirality : 0.048 0.234 997 Planarity : 0.004 0.041 1179 Dihedral : 5.100 40.254 954 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.27 % Allowed : 24.38 % Favored : 71.35 % 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: -2.41 (0.27), residues: 841 helix: -2.86 (2.12), residues: 6 sheet: -0.65 (0.30), residues: 315 loop : -2.32 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 7 HIS 0.003 0.001 HIS A 274 PHE 0.027 0.001 PHE A 410 TYR 0.014 0.001 TYR N 94 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 2.28939 ( 3) hydrogen bonds : bond 0.03293 ( 151) hydrogen bonds : angle 5.56511 ( 423) SS BOND : bond 0.00800 ( 13) SS BOND : angle 2.65477 ( 26) covalent geometry : bond 0.00305 ( 6769) covalent geometry : angle 0.67291 ( 9197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2542.94 seconds wall clock time: 45 minutes 15.20 seconds (2715.20 seconds total)