Starting phenix.real_space_refine on Thu Feb 5 15:31:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oqq_70770/02_2026/9oqq_70770_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oqq_70770/02_2026/9oqq_70770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oqq_70770/02_2026/9oqq_70770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oqq_70770/02_2026/9oqq_70770.map" model { file = "/net/cci-nas-00/data/ceres_data/9oqq_70770/02_2026/9oqq_70770_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oqq_70770/02_2026/9oqq_70770_neut.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 77 5.16 5 C 12096 2.51 5 N 2884 2.21 5 O 3164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18221 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2589 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 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 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.30, per 1000 atoms: 0.13 Number of scatterers: 18221 At special positions: 0 Unit cell: (107.996, 107.996, 120.988, 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 77 16.00 O 3164 8.00 N 2884 7.00 C 12096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 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 701 " - " ASN A 255 " " NAG B 701 " - " ASN B 255 " " NAG C 701 " - " ASN C 255 " " NAG D 701 " - " ASN D 255 " " NAG E 701 " - " ASN E 255 " " NAG F 701 " - " ASN F 255 " " NAG G 701 " - " ASN G 255 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 756.4 milliseconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 7 sheets defined 70.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.630A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 131 Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix removed outlier: 3.717A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.831A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.630A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.947A pdb=" N LEU B 103 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 131 Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix removed outlier: 3.717A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.830A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.681A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.630A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 131 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.620A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix removed outlier: 3.717A pdb=" N PHE C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.831A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.630A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 131 Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix removed outlier: 3.717A pdb=" N PHE D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.831A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.630A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 99 through 108 removed outlier: 3.949A pdb=" N LEU E 103 " --> pdb=" O GLY E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 131 Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 Processing helix chain 'E' and resid 194 through 204 Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix removed outlier: 3.717A pdb=" N PHE E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.831A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.630A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 131 Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.620A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix removed outlier: 3.718A pdb=" N PHE F 296 " --> pdb=" O VAL F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 304 through 312 removed outlier: 4.014A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.830A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.630A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 99 through 108 removed outlier: 3.948A pdb=" N LEU G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 131 Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 254 removed outlier: 3.619A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix removed outlier: 3.717A pdb=" N PHE G 296 " --> pdb=" O VAL G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 304 through 312 removed outlier: 4.013A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.831A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.682A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 1226 hydrogen bonds defined for protein. 3531 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: 3.32 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5462 1.34 - 1.46: 2940 1.46 - 1.57: 10134 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 18627 Sorted by residual: bond pdb=" N ASN E 369 " pdb=" CA ASN E 369 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.17e-02 7.31e+03 9.56e+00 bond pdb=" N ASN C 369 " pdb=" CA ASN C 369 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.17e-02 7.31e+03 9.34e+00 bond pdb=" N ASN D 369 " pdb=" CA ASN D 369 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.17e-02 7.31e+03 9.25e+00 bond pdb=" N ASN G 369 " pdb=" CA ASN G 369 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.17e-02 7.31e+03 9.25e+00 bond pdb=" N ASN A 369 " pdb=" CA ASN A 369 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.17e-02 7.31e+03 9.18e+00 ... (remaining 18622 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 23870 1.48 - 2.96: 1246 2.96 - 4.44: 208 4.44 - 5.92: 79 5.92 - 7.40: 14 Bond angle restraints: 25417 Sorted by residual: angle pdb=" C TYR D 10 " pdb=" N VAL D 11 " pdb=" CA VAL D 11 " ideal model delta sigma weight residual 122.77 118.85 3.92 1.05e+00 9.07e-01 1.39e+01 angle pdb=" CA LEU F 52 " pdb=" C LEU F 52 " pdb=" O LEU F 52 " ideal model delta sigma weight residual 120.70 116.87 3.83 1.03e+00 9.43e-01 1.39e+01 angle pdb=" C TYR A 10 " pdb=" N VAL A 11 " pdb=" CA VAL A 11 " ideal model delta sigma weight residual 122.77 118.87 3.90 1.05e+00 9.07e-01 1.38e+01 angle pdb=" C TYR B 10 " pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 122.77 118.87 3.90 1.05e+00 9.07e-01 1.38e+01 angle pdb=" C TYR C 10 " pdb=" N VAL C 11 " pdb=" CA VAL C 11 " ideal model delta sigma weight residual 122.77 118.87 3.90 1.05e+00 9.07e-01 1.38e+01 ... (remaining 25412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 10164 15.42 - 30.84: 798 30.84 - 46.26: 216 46.26 - 61.68: 36 61.68 - 77.09: 7 Dihedral angle restraints: 11221 sinusoidal: 4046 harmonic: 7175 Sorted by residual: dihedral pdb=" CA SER B 322 " pdb=" C SER B 322 " pdb=" N GLU B 323 " pdb=" CA GLU B 323 " ideal model delta harmonic sigma weight residual 180.00 164.30 15.70 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CA SER F 322 " pdb=" C SER F 322 " pdb=" N GLU F 323 " pdb=" CA GLU F 323 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 dihedral pdb=" CA SER E 322 " pdb=" C SER E 322 " pdb=" N GLU E 323 " pdb=" CA GLU E 323 " ideal model delta harmonic sigma weight residual 180.00 164.33 15.67 0 5.00e+00 4.00e-02 9.82e+00 ... (remaining 11218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2402 0.049 - 0.098: 587 0.098 - 0.147: 103 0.147 - 0.196: 16 0.196 - 0.245: 7 Chirality restraints: 3115 Sorted by residual: chirality pdb=" CA LEU E 52 " pdb=" N LEU E 52 " pdb=" C LEU E 52 " pdb=" CB LEU E 52 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LEU F 52 " pdb=" N LEU F 52 " pdb=" C LEU F 52 " pdb=" CB LEU F 52 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3112 not shown) Planarity restraints: 3122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 701 " -0.090 2.00e-02 2.50e+03 7.35e-02 6.76e+01 pdb=" C7 NAG C 701 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG C 701 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG C 701 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG C 701 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 701 " -0.090 2.00e-02 2.50e+03 7.35e-02 6.76e+01 pdb=" C7 NAG G 701 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG G 701 " -0.068 2.00e-02 2.50e+03 pdb=" N2 NAG G 701 " 0.116 2.00e-02 2.50e+03 pdb=" O7 NAG G 701 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 701 " 0.090 2.00e-02 2.50e+03 7.35e-02 6.76e+01 pdb=" C7 NAG F 701 " -0.026 2.00e-02 2.50e+03 pdb=" C8 NAG F 701 " 0.068 2.00e-02 2.50e+03 pdb=" N2 NAG F 701 " -0.116 2.00e-02 2.50e+03 pdb=" O7 NAG F 701 " -0.016 2.00e-02 2.50e+03 ... (remaining 3119 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4575 2.79 - 3.31: 19218 3.31 - 3.84: 31147 3.84 - 4.37: 35848 4.37 - 4.90: 61873 Nonbonded interactions: 152661 Sorted by model distance: nonbonded pdb=" OD1 ASN C 151 " pdb=" O MET C 372 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN D 151 " pdb=" O MET D 372 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN F 151 " pdb=" O MET F 372 " model vdw 2.258 3.040 nonbonded pdb=" OD1 ASN A 151 " pdb=" O MET A 372 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASN G 151 " pdb=" O MET G 372 " model vdw 2.259 3.040 ... (remaining 152656 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 0.037 18648 Z= 0.311 Angle : 0.782 7.404 25466 Z= 0.490 Chirality : 0.045 0.245 3115 Planarity : 0.005 0.074 3115 Dihedral : 12.530 77.094 6517 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.15 % Allowed : 6.11 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2380 helix: -0.03 (0.12), residues: 1603 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 152 TYR 0.014 0.002 TYR B 10 PHE 0.012 0.002 PHE D 54 TRP 0.008 0.001 TRP E 104 HIS 0.002 0.001 HIS C 106 Details of bonding type rmsd covalent geometry : bond 0.00610 (18627) covalent geometry : angle 0.78169 (25417) SS BOND : bond 0.00282 ( 14) SS BOND : angle 0.73851 ( 28) hydrogen bonds : bond 0.14060 ( 1226) hydrogen bonds : angle 5.47868 ( 3531) link_NAG-ASN : bond 0.00522 ( 7) link_NAG-ASN : angle 0.87715 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 616 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8546 (m-30) cc_final: 0.8328 (m-30) REVERT: C 230 TYR cc_start: 0.8921 (t80) cc_final: 0.8715 (t80) REVERT: D 230 TYR cc_start: 0.8928 (t80) cc_final: 0.8707 (t80) REVERT: F 230 TYR cc_start: 0.8955 (t80) cc_final: 0.8553 (t80) outliers start: 21 outliers final: 0 residues processed: 616 average time/residue: 0.1422 time to fit residues: 127.9823 Evaluate side-chains 418 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 90 GLN A 274 GLN B 76 GLN B 274 GLN C 76 GLN C 274 GLN C 280 ASN D 76 GLN D 274 GLN E 76 GLN E 274 GLN F 76 GLN F 274 GLN G 76 GLN G 90 GLN G 274 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.115756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091799 restraints weight = 39171.411| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.19 r_work: 0.3281 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18648 Z= 0.165 Angle : 0.662 9.061 25466 Z= 0.322 Chirality : 0.042 0.153 3115 Planarity : 0.004 0.036 3115 Dihedral : 4.275 15.854 2709 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.54 % Allowed : 16.68 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2380 helix: 1.42 (0.13), residues: 1589 sheet: None (None), residues: 0 loop : -2.33 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 217 TYR 0.021 0.001 TYR B 230 PHE 0.008 0.001 PHE G 54 TRP 0.008 0.001 TRP C 104 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00379 (18627) covalent geometry : angle 0.66053 (25417) SS BOND : bond 0.00347 ( 14) SS BOND : angle 0.72969 ( 28) hydrogen bonds : bond 0.03939 ( 1226) hydrogen bonds : angle 4.11168 ( 3531) link_NAG-ASN : bond 0.00496 ( 7) link_NAG-ASN : angle 1.36543 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 456 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASP cc_start: 0.8360 (m-30) cc_final: 0.8085 (t0) REVERT: A 57 GLU cc_start: 0.8465 (pm20) cc_final: 0.8004 (pm20) REVERT: A 217 ARG cc_start: 0.8919 (mmp80) cc_final: 0.8446 (mmp80) REVERT: A 264 GLN cc_start: 0.8807 (tp40) cc_final: 0.7688 (tp40) REVERT: B 9 GLU cc_start: 0.8683 (tt0) cc_final: 0.8429 (tt0) REVERT: B 35 ASP cc_start: 0.8445 (m-30) cc_final: 0.8178 (t0) REVERT: B 140 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8633 (ptpp) REVERT: B 217 ARG cc_start: 0.8919 (mmp80) cc_final: 0.8375 (mmp80) REVERT: B 264 GLN cc_start: 0.8784 (tp40) cc_final: 0.8287 (tp40) REVERT: B 355 LYS cc_start: 0.6244 (tptp) cc_final: 0.5567 (mmmt) REVERT: C 230 TYR cc_start: 0.9197 (t80) cc_final: 0.8973 (t80) REVERT: C 264 GLN cc_start: 0.8750 (tp40) cc_final: 0.7711 (tp40) REVERT: D 35 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: D 57 GLU cc_start: 0.8374 (pm20) cc_final: 0.7764 (pm20) REVERT: D 230 TYR cc_start: 0.9234 (t80) cc_final: 0.9010 (t80) REVERT: E 35 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (m-30) REVERT: F 35 ASP cc_start: 0.8337 (m-30) cc_final: 0.8046 (m-30) REVERT: F 217 ARG cc_start: 0.8855 (mmp80) cc_final: 0.8467 (mmp80) REVERT: F 230 TYR cc_start: 0.9178 (t80) cc_final: 0.8782 (t80) REVERT: F 264 GLN cc_start: 0.8800 (tp40) cc_final: 0.7814 (tp40) REVERT: G 35 ASP cc_start: 0.8343 (m-30) cc_final: 0.7987 (t0) REVERT: G 140 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8794 (ptpp) REVERT: G 152 ARG cc_start: 0.5124 (mtp85) cc_final: 0.4819 (mtt180) REVERT: G 217 ARG cc_start: 0.8870 (mmp80) cc_final: 0.8330 (mmp80) outliers start: 65 outliers final: 34 residues processed: 503 average time/residue: 0.1428 time to fit residues: 108.0641 Evaluate side-chains 441 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 403 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 295 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 139 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 89 GLN B 332 ASN C 134 HIS C 280 ASN C 332 ASN D 89 GLN D 332 ASN E 89 GLN ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 ASN F 332 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086742 restraints weight = 40420.206| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.12 r_work: 0.3182 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18648 Z= 0.270 Angle : 0.714 12.245 25466 Z= 0.348 Chirality : 0.046 0.283 3115 Planarity : 0.004 0.033 3115 Dihedral : 4.704 24.821 2709 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.11 % Allowed : 17.01 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2380 helix: 1.48 (0.14), residues: 1596 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 75 TYR 0.021 0.002 TYR A 345 PHE 0.016 0.002 PHE B 54 TRP 0.010 0.002 TRP E 104 HIS 0.003 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00629 (18627) covalent geometry : angle 0.71396 (25417) SS BOND : bond 0.00405 ( 14) SS BOND : angle 0.86784 ( 28) hydrogen bonds : bond 0.04196 ( 1226) hydrogen bonds : angle 4.32857 ( 3531) link_NAG-ASN : bond 0.00147 ( 7) link_NAG-ASN : angle 0.97892 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 427 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8690 (tpp) cc_final: 0.8126 (tmm) REVERT: A 310 GLU cc_start: 0.7048 (tp30) cc_final: 0.6232 (pm20) REVERT: A 337 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 347 CYS cc_start: 0.9187 (m) cc_final: 0.8943 (m) REVERT: A 352 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8133 (mm-30) REVERT: B 9 GLU cc_start: 0.8782 (tt0) cc_final: 0.8468 (tt0) REVERT: B 89 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8165 (mm110) REVERT: B 256 ASP cc_start: 0.7323 (t70) cc_final: 0.7051 (t0) REVERT: B 310 GLU cc_start: 0.6968 (tp30) cc_final: 0.6206 (pm20) REVERT: B 337 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 352 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 37 MET cc_start: 0.8745 (tpp) cc_final: 0.8065 (tmm) REVERT: C 140 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9007 (ptpp) REVERT: C 333 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8456 (mm) REVERT: C 337 GLU cc_start: 0.8371 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 37 MET cc_start: 0.8727 (tpp) cc_final: 0.8099 (tmm) REVERT: D 89 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8140 (mm110) REVERT: D 230 TYR cc_start: 0.9320 (t80) cc_final: 0.9108 (t80) REVERT: D 310 GLU cc_start: 0.7084 (tp30) cc_final: 0.6268 (pm20) REVERT: D 337 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7950 (tm-30) REVERT: D 347 CYS cc_start: 0.9132 (m) cc_final: 0.8882 (m) REVERT: D 352 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7867 (mm-30) REVERT: E 37 MET cc_start: 0.8749 (tpp) cc_final: 0.8195 (tmm) REVERT: E 89 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8033 (mm110) REVERT: E 140 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8972 (ptpp) REVERT: E 310 GLU cc_start: 0.6917 (tp30) cc_final: 0.6192 (pm20) REVERT: E 337 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8001 (tm-30) REVERT: E 352 GLU cc_start: 0.8720 (mm-30) cc_final: 0.7928 (mm-30) REVERT: F 310 GLU cc_start: 0.6839 (tp30) cc_final: 0.6285 (pm20) REVERT: F 337 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7843 (tm-30) REVERT: F 352 GLU cc_start: 0.8676 (mm-30) cc_final: 0.7975 (mm-30) REVERT: G 140 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8891 (ptpp) REVERT: G 152 ARG cc_start: 0.5195 (mtp85) cc_final: 0.4799 (mtt-85) REVERT: G 217 ARG cc_start: 0.8852 (mmp80) cc_final: 0.8620 (mmp80) REVERT: G 306 LEU cc_start: 0.7315 (mt) cc_final: 0.6533 (tt) REVERT: G 310 GLU cc_start: 0.6986 (tp30) cc_final: 0.6211 (pm20) REVERT: G 337 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7813 (tm-30) REVERT: G 352 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8095 (mm-30) outliers start: 112 outliers final: 71 residues processed: 502 average time/residue: 0.1348 time to fit residues: 101.9591 Evaluate side-chains 476 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 398 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 225 LEU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 295 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.0050 chunk 204 optimal weight: 0.0010 chunk 225 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 186 optimal weight: 8.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN D 89 GLN D 134 HIS D 353 ASN E 89 GLN E 134 HIS E 280 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091302 restraints weight = 39443.045| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.13 r_work: 0.3276 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18648 Z= 0.119 Angle : 0.600 8.758 25466 Z= 0.290 Chirality : 0.042 0.261 3115 Planarity : 0.004 0.037 3115 Dihedral : 4.055 17.045 2709 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.49 % Allowed : 21.10 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.19), residues: 2380 helix: 2.02 (0.14), residues: 1575 sheet: None (None), residues: 0 loop : -1.53 (0.23), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 217 TYR 0.015 0.001 TYR A 345 PHE 0.010 0.001 PHE B 54 TRP 0.012 0.001 TRP D 104 HIS 0.003 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00262 (18627) covalent geometry : angle 0.60006 (25417) SS BOND : bond 0.00105 ( 14) SS BOND : angle 0.36440 ( 28) hydrogen bonds : bond 0.03206 ( 1226) hydrogen bonds : angle 3.96245 ( 3531) link_NAG-ASN : bond 0.00435 ( 7) link_NAG-ASN : angle 0.97949 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 460 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9189 (tt0) cc_final: 0.8985 (tt0) REVERT: A 37 MET cc_start: 0.8676 (tpp) cc_final: 0.8082 (tmm) REVERT: A 39 THR cc_start: 0.9039 (m) cc_final: 0.8832 (t) REVERT: A 200 LEU cc_start: 0.8073 (mm) cc_final: 0.7539 (tt) REVERT: A 230 TYR cc_start: 0.9168 (t80) cc_final: 0.8933 (t80) REVERT: A 337 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 347 CYS cc_start: 0.9170 (m) cc_final: 0.8907 (m) REVERT: B 9 GLU cc_start: 0.8835 (tt0) cc_final: 0.8448 (tt0) REVERT: B 39 THR cc_start: 0.9060 (m) cc_final: 0.8851 (t) REVERT: B 200 LEU cc_start: 0.8194 (mm) cc_final: 0.7575 (tt) REVERT: B 256 ASP cc_start: 0.7326 (t70) cc_final: 0.7059 (t0) REVERT: B 310 GLU cc_start: 0.6918 (tp30) cc_final: 0.6301 (pm20) REVERT: B 337 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 352 GLU cc_start: 0.8719 (mm-30) cc_final: 0.7997 (mm-30) REVERT: C 37 MET cc_start: 0.8666 (tpp) cc_final: 0.8072 (tmm) REVERT: C 140 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8984 (ptpp) REVERT: C 200 LEU cc_start: 0.8085 (mm) cc_final: 0.7567 (tt) REVERT: D 37 MET cc_start: 0.8736 (tpp) cc_final: 0.8047 (tmm) REVERT: D 143 MET cc_start: 0.9066 (mtm) cc_final: 0.8789 (mmm) REVERT: D 200 LEU cc_start: 0.8169 (mm) cc_final: 0.7593 (tt) REVERT: D 230 TYR cc_start: 0.9181 (t80) cc_final: 0.8958 (t80) REVERT: D 310 GLU cc_start: 0.6831 (tp30) cc_final: 0.6284 (pm20) REVERT: D 337 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7837 (tm-30) REVERT: D 347 CYS cc_start: 0.9094 (m) cc_final: 0.8806 (m) REVERT: D 352 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7975 (mm-30) REVERT: E 9 GLU cc_start: 0.9010 (tt0) cc_final: 0.8656 (tt0) REVERT: E 140 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9051 (ptpp) REVERT: E 200 LEU cc_start: 0.8168 (mm) cc_final: 0.7627 (tt) REVERT: E 310 GLU cc_start: 0.6980 (tp30) cc_final: 0.6416 (pm20) REVERT: E 337 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7763 (tm-30) REVERT: E 352 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8198 (mm-30) REVERT: F 129 PHE cc_start: 0.9183 (m-80) cc_final: 0.8811 (m-10) REVERT: F 143 MET cc_start: 0.9157 (mtm) cc_final: 0.8951 (mtp) REVERT: F 200 LEU cc_start: 0.8097 (mm) cc_final: 0.7574 (tt) REVERT: F 230 TYR cc_start: 0.9117 (t80) cc_final: 0.8722 (t80) REVERT: F 310 GLU cc_start: 0.6865 (tp30) cc_final: 0.6437 (pm20) REVERT: F 337 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7753 (tm-30) REVERT: F 352 GLU cc_start: 0.8708 (mm-30) cc_final: 0.7902 (mm-30) REVERT: G 35 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8134 (t0) REVERT: G 140 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8891 (ptpp) REVERT: G 200 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7493 (tt) REVERT: G 217 ARG cc_start: 0.8776 (mmp80) cc_final: 0.8423 (mmp80) REVERT: G 310 GLU cc_start: 0.6889 (tp30) cc_final: 0.6305 (pm20) REVERT: G 352 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8005 (mm-30) outliers start: 64 outliers final: 31 residues processed: 500 average time/residue: 0.1365 time to fit residues: 103.9697 Evaluate side-chains 454 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 418 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain E residue 134 HIS Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 203 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 208 ASN B 89 GLN B 134 HIS C 89 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN F 134 HIS F 208 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.112725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089943 restraints weight = 39781.240| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.10 r_work: 0.3248 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18648 Z= 0.140 Angle : 0.615 9.924 25466 Z= 0.296 Chirality : 0.043 0.268 3115 Planarity : 0.004 0.036 3115 Dihedral : 4.012 15.155 2709 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.02 % Allowed : 21.65 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 2380 helix: 2.08 (0.14), residues: 1575 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 75 TYR 0.015 0.001 TYR A 345 PHE 0.012 0.001 PHE B 54 TRP 0.010 0.001 TRP C 104 HIS 0.013 0.002 HIS E 134 Details of bonding type rmsd covalent geometry : bond 0.00331 (18627) covalent geometry : angle 0.61422 (25417) SS BOND : bond 0.00212 ( 14) SS BOND : angle 0.50500 ( 28) hydrogen bonds : bond 0.03321 ( 1226) hydrogen bonds : angle 4.00388 ( 3531) link_NAG-ASN : bond 0.00313 ( 7) link_NAG-ASN : angle 1.07539 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 441 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLU cc_start: 0.9189 (tt0) cc_final: 0.8920 (tt0) REVERT: A 200 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7579 (tt) REVERT: A 230 TYR cc_start: 0.9209 (t80) cc_final: 0.8967 (t80) REVERT: A 310 GLU cc_start: 0.7117 (tp30) cc_final: 0.6373 (pm20) REVERT: A 347 CYS cc_start: 0.9178 (m) cc_final: 0.8918 (m) REVERT: A 352 GLU cc_start: 0.8706 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 9 GLU cc_start: 0.8868 (tt0) cc_final: 0.8509 (tt0) REVERT: B 39 THR cc_start: 0.9150 (m) cc_final: 0.8913 (t) REVERT: B 140 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8826 (ptpp) REVERT: B 200 LEU cc_start: 0.8194 (mm) cc_final: 0.7586 (tt) REVERT: B 256 ASP cc_start: 0.7365 (t70) cc_final: 0.7046 (t0) REVERT: B 310 GLU cc_start: 0.6941 (tp30) cc_final: 0.6369 (pm20) REVERT: B 337 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7835 (tm-30) REVERT: B 352 GLU cc_start: 0.8712 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 140 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8993 (ptpp) REVERT: C 200 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7534 (tt) REVERT: C 337 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 37 MET cc_start: 0.8728 (tpp) cc_final: 0.8056 (tmm) REVERT: D 143 MET cc_start: 0.9084 (mtm) cc_final: 0.8770 (mmm) REVERT: D 200 LEU cc_start: 0.8131 (mm) cc_final: 0.7536 (tt) REVERT: D 230 TYR cc_start: 0.9212 (t80) cc_final: 0.8989 (t80) REVERT: D 310 GLU cc_start: 0.6902 (tp30) cc_final: 0.6381 (pm20) REVERT: D 337 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7777 (tm-30) REVERT: D 347 CYS cc_start: 0.9140 (m) cc_final: 0.8857 (m) REVERT: D 352 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7961 (mm-30) REVERT: E 37 MET cc_start: 0.8748 (tpp) cc_final: 0.8087 (tmm) REVERT: E 140 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9045 (ptpp) REVERT: E 200 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7540 (tt) REVERT: E 310 GLU cc_start: 0.6903 (tp30) cc_final: 0.6364 (pm20) REVERT: E 337 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7829 (tm-30) REVERT: E 352 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8250 (mm-30) REVERT: F 200 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7567 (tt) REVERT: F 230 TYR cc_start: 0.9150 (t80) cc_final: 0.8787 (t80) REVERT: F 310 GLU cc_start: 0.6920 (tp30) cc_final: 0.6526 (pm20) REVERT: F 337 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7709 (tm-30) REVERT: F 352 GLU cc_start: 0.8694 (mm-30) cc_final: 0.7924 (mm-30) REVERT: G 35 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8120 (t0) REVERT: G 140 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8886 (ptpp) REVERT: G 200 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7580 (tt) REVERT: G 217 ARG cc_start: 0.8798 (mmp80) cc_final: 0.8449 (mmp80) REVERT: G 256 ASP cc_start: 0.7982 (t70) cc_final: 0.7373 (t0) REVERT: G 310 GLU cc_start: 0.6825 (tp30) cc_final: 0.6326 (pm20) REVERT: G 337 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7690 (tm-30) REVERT: G 352 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8074 (mm-30) outliers start: 92 outliers final: 65 residues processed: 500 average time/residue: 0.1358 time to fit residues: 103.7263 Evaluate side-chains 491 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 416 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 134 HIS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 117 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 169 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN D 134 HIS E 89 GLN E 208 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.121857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.099430 restraints weight = 39969.314| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.05 r_work: 0.3448 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18648 Z= 0.118 Angle : 0.601 9.087 25466 Z= 0.287 Chirality : 0.042 0.231 3115 Planarity : 0.004 0.036 3115 Dihedral : 3.869 17.428 2709 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.87 % Allowed : 23.56 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.19), residues: 2380 helix: 2.16 (0.14), residues: 1568 sheet: None (None), residues: 0 loop : -1.37 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 75 TYR 0.022 0.001 TYR G 10 PHE 0.009 0.001 PHE B 54 TRP 0.012 0.001 TRP C 104 HIS 0.011 0.002 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00267 (18627) covalent geometry : angle 0.60052 (25417) SS BOND : bond 0.00134 ( 14) SS BOND : angle 0.37831 ( 28) hydrogen bonds : bond 0.03153 ( 1226) hydrogen bonds : angle 3.96406 ( 3531) link_NAG-ASN : bond 0.00361 ( 7) link_NAG-ASN : angle 1.09363 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 457 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.9007 (mtm) cc_final: 0.8705 (mmm) REVERT: A 200 LEU cc_start: 0.8141 (mm) cc_final: 0.7607 (tt) REVERT: A 230 TYR cc_start: 0.9062 (t80) cc_final: 0.8826 (t80) REVERT: A 306 LEU cc_start: 0.6956 (mt) cc_final: 0.6396 (tt) REVERT: A 310 GLU cc_start: 0.7049 (tp30) cc_final: 0.6440 (pm20) REVERT: A 347 CYS cc_start: 0.9167 (m) cc_final: 0.8900 (m) REVERT: A 352 GLU cc_start: 0.8678 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 9 GLU cc_start: 0.8645 (tt0) cc_final: 0.8350 (tt0) REVERT: B 39 THR cc_start: 0.9127 (m) cc_final: 0.8879 (t) REVERT: B 200 LEU cc_start: 0.8262 (mm) cc_final: 0.7647 (tt) REVERT: B 256 ASP cc_start: 0.7164 (t70) cc_final: 0.6907 (t0) REVERT: B 306 LEU cc_start: 0.7047 (mt) cc_final: 0.6492 (tt) REVERT: B 310 GLU cc_start: 0.6877 (tp30) cc_final: 0.6414 (pm20) REVERT: B 352 GLU cc_start: 0.8627 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 140 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8972 (ptpp) REVERT: C 200 LEU cc_start: 0.8122 (mm) cc_final: 0.7586 (tt) REVERT: C 337 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 37 MET cc_start: 0.8732 (tpp) cc_final: 0.8209 (tmm) REVERT: D 39 THR cc_start: 0.9150 (m) cc_final: 0.8907 (t) REVERT: D 143 MET cc_start: 0.9023 (mtm) cc_final: 0.8743 (mmm) REVERT: D 200 LEU cc_start: 0.8183 (mm) cc_final: 0.7609 (tt) REVERT: D 230 TYR cc_start: 0.9085 (t80) cc_final: 0.8882 (t80) REVERT: D 310 GLU cc_start: 0.6834 (tp30) cc_final: 0.6413 (pm20) REVERT: D 337 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7726 (tm-30) REVERT: D 347 CYS cc_start: 0.9053 (m) cc_final: 0.8726 (m) REVERT: D 352 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7914 (mm-30) REVERT: E 3 ILE cc_start: 0.9515 (mm) cc_final: 0.9082 (mm) REVERT: E 37 MET cc_start: 0.8791 (tpp) cc_final: 0.8126 (tmm) REVERT: E 89 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8018 (mm110) REVERT: E 140 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9097 (ptpp) REVERT: E 200 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7613 (tt) REVERT: E 310 GLU cc_start: 0.6870 (tp30) cc_final: 0.6454 (pm20) REVERT: E 337 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7712 (tm-30) REVERT: E 352 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8183 (mm-30) REVERT: F 3 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9036 (mp) REVERT: F 39 THR cc_start: 0.9145 (m) cc_final: 0.8936 (t) REVERT: F 143 MET cc_start: 0.9143 (mtp) cc_final: 0.8926 (mmm) REVERT: F 200 LEU cc_start: 0.8171 (mm) cc_final: 0.7671 (tt) REVERT: F 230 TYR cc_start: 0.8995 (t80) cc_final: 0.8625 (t80) REVERT: F 306 LEU cc_start: 0.7144 (mt) cc_final: 0.6465 (tt) REVERT: F 310 GLU cc_start: 0.6896 (tp30) cc_final: 0.6597 (pm20) REVERT: F 337 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7712 (tm-30) REVERT: F 352 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7889 (mm-30) REVERT: G 9 GLU cc_start: 0.9046 (tt0) cc_final: 0.8730 (tt0) REVERT: G 35 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8134 (t0) REVERT: G 136 CYS cc_start: 0.9395 (t) cc_final: 0.9192 (p) REVERT: G 140 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9019 (ptpp) REVERT: G 200 LEU cc_start: 0.8194 (mm) cc_final: 0.7703 (tt) REVERT: G 217 ARG cc_start: 0.8756 (mmp80) cc_final: 0.8383 (mmp80) REVERT: G 256 ASP cc_start: 0.7778 (t70) cc_final: 0.7238 (t0) REVERT: G 310 GLU cc_start: 0.6808 (tp30) cc_final: 0.6408 (pm20) REVERT: G 352 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7900 (mm-30) outliers start: 71 outliers final: 56 residues processed: 503 average time/residue: 0.1335 time to fit residues: 103.1048 Evaluate side-chains 486 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 423 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 134 HIS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 117 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 103 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 229 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 198 GLN B 198 GLN B 280 ASN C 198 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN D 198 GLN E 89 GLN E 134 HIS E 198 GLN F 134 HIS F 198 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 198 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.117771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094915 restraints weight = 41153.119| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.05 r_work: 0.3367 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18648 Z= 0.226 Angle : 0.684 10.761 25466 Z= 0.331 Chirality : 0.045 0.313 3115 Planarity : 0.004 0.036 3115 Dihedral : 4.364 20.805 2709 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.07 % Allowed : 22.79 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.18), residues: 2380 helix: 1.98 (0.14), residues: 1547 sheet: None (None), residues: 0 loop : -1.34 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 217 TYR 0.022 0.002 TYR A 10 PHE 0.018 0.001 PHE E 54 TRP 0.007 0.002 TRP G 127 HIS 0.009 0.002 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00533 (18627) covalent geometry : angle 0.68314 (25417) SS BOND : bond 0.00437 ( 14) SS BOND : angle 0.88134 ( 28) hydrogen bonds : bond 0.03679 ( 1226) hydrogen bonds : angle 4.19352 ( 3531) link_NAG-ASN : bond 0.00153 ( 7) link_NAG-ASN : angle 1.16637 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 424 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8393 (pm20) cc_final: 0.8011 (pm20) REVERT: A 143 MET cc_start: 0.9050 (mtm) cc_final: 0.8723 (mmm) REVERT: A 310 GLU cc_start: 0.7043 (tp30) cc_final: 0.6434 (pm20) REVERT: A 337 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7718 (tm-30) REVERT: A 347 CYS cc_start: 0.9229 (m) cc_final: 0.8991 (m) REVERT: A 352 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 39 THR cc_start: 0.9230 (m) cc_final: 0.9006 (t) REVERT: B 256 ASP cc_start: 0.7351 (t70) cc_final: 0.7061 (t0) REVERT: B 310 GLU cc_start: 0.6856 (tp30) cc_final: 0.6368 (pm20) REVERT: B 337 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7841 (tm-30) REVERT: B 352 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 57 GLU cc_start: 0.8425 (pm20) cc_final: 0.7701 (pm20) REVERT: C 200 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7682 (tt) REVERT: C 306 LEU cc_start: 0.7298 (mt) cc_final: 0.6685 (tt) REVERT: C 310 GLU cc_start: 0.6775 (tp30) cc_final: 0.6341 (pm20) REVERT: C 337 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7732 (tm-30) REVERT: C 352 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7575 (mm-30) REVERT: D 39 THR cc_start: 0.9217 (m) cc_final: 0.8989 (t) REVERT: D 57 GLU cc_start: 0.8225 (pm20) cc_final: 0.7751 (pm20) REVERT: D 143 MET cc_start: 0.9115 (mtm) cc_final: 0.8849 (mmm) REVERT: D 230 TYR cc_start: 0.9170 (t80) cc_final: 0.8964 (t80) REVERT: D 306 LEU cc_start: 0.7352 (mt) cc_final: 0.6672 (tt) REVERT: D 310 GLU cc_start: 0.6944 (tp30) cc_final: 0.6385 (pm20) REVERT: D 337 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7838 (tm-30) REVERT: D 347 CYS cc_start: 0.9118 (m) cc_final: 0.8810 (m) REVERT: D 352 GLU cc_start: 0.8604 (mm-30) cc_final: 0.7960 (mm-30) REVERT: E 37 MET cc_start: 0.8755 (tpp) cc_final: 0.8213 (tmm) REVERT: E 57 GLU cc_start: 0.8261 (pm20) cc_final: 0.7974 (pm20) REVERT: E 89 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7989 (mm110) REVERT: E 140 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9105 (ptpp) REVERT: E 306 LEU cc_start: 0.7176 (mt) cc_final: 0.6395 (tt) REVERT: E 310 GLU cc_start: 0.6804 (tp30) cc_final: 0.6352 (pm20) REVERT: E 337 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7733 (tm-30) REVERT: E 352 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8247 (tp30) REVERT: F 310 GLU cc_start: 0.6890 (tp30) cc_final: 0.6526 (pm20) REVERT: F 337 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7703 (tm-30) REVERT: F 352 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7932 (mm-30) REVERT: G 37 MET cc_start: 0.8476 (tpp) cc_final: 0.8112 (tmm) REVERT: G 140 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8930 (ptpp) REVERT: G 217 ARG cc_start: 0.8788 (mmp80) cc_final: 0.8515 (mmp80) REVERT: G 256 ASP cc_start: 0.7849 (t70) cc_final: 0.7333 (t0) REVERT: G 306 LEU cc_start: 0.7068 (mt) cc_final: 0.6465 (tt) REVERT: G 310 GLU cc_start: 0.6770 (tp30) cc_final: 0.6343 (pm20) REVERT: G 337 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7706 (tm-30) REVERT: G 352 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8003 (mm-30) outliers start: 93 outliers final: 71 residues processed: 483 average time/residue: 0.1362 time to fit residues: 100.7513 Evaluate side-chains 488 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 413 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 261 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 139 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS C 134 HIS C 353 ASN D 134 HIS E 89 GLN F 353 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.121441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.099107 restraints weight = 40556.030| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.98 r_work: 0.3431 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18648 Z= 0.130 Angle : 0.626 8.991 25466 Z= 0.301 Chirality : 0.044 0.328 3115 Planarity : 0.004 0.036 3115 Dihedral : 4.065 20.497 2709 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.20 % Allowed : 24.54 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.18), residues: 2380 helix: 1.95 (0.14), residues: 1561 sheet: None (None), residues: 0 loop : -1.37 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 217 TYR 0.020 0.001 TYR A 10 PHE 0.011 0.001 PHE E 54 TRP 0.012 0.001 TRP E 104 HIS 0.004 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00301 (18627) covalent geometry : angle 0.62545 (25417) SS BOND : bond 0.00132 ( 14) SS BOND : angle 0.45864 ( 28) hydrogen bonds : bond 0.03196 ( 1226) hydrogen bonds : angle 4.06143 ( 3531) link_NAG-ASN : bond 0.00357 ( 7) link_NAG-ASN : angle 1.05819 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 450 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 VAL cc_start: 0.9643 (m) cc_final: 0.9351 (p) REVERT: A 57 GLU cc_start: 0.8108 (pm20) cc_final: 0.7846 (pm20) REVERT: A 143 MET cc_start: 0.8984 (mtm) cc_final: 0.8708 (mmm) REVERT: A 200 LEU cc_start: 0.8170 (mm) cc_final: 0.7637 (tt) REVERT: A 230 TYR cc_start: 0.9105 (t80) cc_final: 0.8882 (t80) REVERT: A 310 GLU cc_start: 0.7142 (tp30) cc_final: 0.6499 (pm20) REVERT: A 347 CYS cc_start: 0.9211 (m) cc_final: 0.8968 (m) REVERT: A 352 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 9 GLU cc_start: 0.8799 (tt0) cc_final: 0.8372 (tt0) REVERT: B 10 TYR cc_start: 0.8710 (m-80) cc_final: 0.7823 (m-80) REVERT: B 39 THR cc_start: 0.9113 (m) cc_final: 0.8856 (t) REVERT: B 57 GLU cc_start: 0.8314 (pm20) cc_final: 0.7524 (pm20) REVERT: B 200 LEU cc_start: 0.8213 (mm) cc_final: 0.7673 (tt) REVERT: B 256 ASP cc_start: 0.7271 (t70) cc_final: 0.6984 (t0) REVERT: B 310 GLU cc_start: 0.6920 (tp30) cc_final: 0.6523 (pm20) REVERT: B 337 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 352 GLU cc_start: 0.8644 (mm-30) cc_final: 0.7953 (mm-30) REVERT: C 140 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9117 (ptpp) REVERT: C 200 LEU cc_start: 0.8151 (mm) cc_final: 0.7681 (tt) REVERT: C 337 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7614 (tm-30) REVERT: D 39 THR cc_start: 0.9109 (m) cc_final: 0.8889 (t) REVERT: D 57 GLU cc_start: 0.8154 (pm20) cc_final: 0.7876 (pm20) REVERT: D 200 LEU cc_start: 0.8246 (mm) cc_final: 0.7669 (tt) REVERT: D 306 LEU cc_start: 0.7236 (mt) cc_final: 0.6619 (tt) REVERT: D 310 GLU cc_start: 0.6897 (tp30) cc_final: 0.6446 (pm20) REVERT: D 337 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 347 CYS cc_start: 0.9102 (m) cc_final: 0.8805 (m) REVERT: D 352 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7938 (mm-30) REVERT: E 37 MET cc_start: 0.8764 (tpp) cc_final: 0.8184 (tmm) REVERT: E 89 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8378 (mm110) REVERT: E 140 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.9091 (ptpp) REVERT: E 200 LEU cc_start: 0.8261 (mm) cc_final: 0.7691 (tt) REVERT: E 310 GLU cc_start: 0.6834 (tp30) cc_final: 0.6404 (pm20) REVERT: E 337 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7668 (tm-30) REVERT: E 352 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8205 (tp30) REVERT: F 200 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7797 (tt) REVERT: F 310 GLU cc_start: 0.6910 (tp30) cc_final: 0.6608 (pm20) REVERT: F 337 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7732 (tm-30) REVERT: F 352 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7879 (mm-30) REVERT: G 35 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8119 (t0) REVERT: G 37 MET cc_start: 0.8457 (tpp) cc_final: 0.8080 (tmm) REVERT: G 140 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8964 (ptpp) REVERT: G 217 ARG cc_start: 0.8756 (mmp80) cc_final: 0.8369 (mmp80) REVERT: G 256 ASP cc_start: 0.7828 (t70) cc_final: 0.7303 (t0) REVERT: G 306 LEU cc_start: 0.7013 (mt) cc_final: 0.6486 (tt) REVERT: G 310 GLU cc_start: 0.6791 (tp30) cc_final: 0.6415 (pm20) REVERT: G 337 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7632 (tm-30) REVERT: G 352 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7956 (mm-30) outliers start: 77 outliers final: 59 residues processed: 501 average time/residue: 0.1243 time to fit residues: 95.8385 Evaluate side-chains 496 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 431 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 217 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 135 optimal weight: 0.1980 chunk 215 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 89 GLN B 353 ASN C 134 HIS E 89 GLN E 134 HIS F 134 HIS ** G 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 353 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.100335 restraints weight = 40570.678| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.04 r_work: 0.3453 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18648 Z= 0.121 Angle : 0.633 8.799 25466 Z= 0.304 Chirality : 0.044 0.323 3115 Planarity : 0.004 0.037 3115 Dihedral : 3.916 20.355 2709 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.93 % Allowed : 25.30 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.18), residues: 2380 helix: 2.00 (0.14), residues: 1554 sheet: None (None), residues: 0 loop : -1.26 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 217 TYR 0.020 0.001 TYR A 10 PHE 0.010 0.001 PHE D 54 TRP 0.010 0.001 TRP C 104 HIS 0.011 0.002 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00273 (18627) covalent geometry : angle 0.63229 (25417) SS BOND : bond 0.00117 ( 14) SS BOND : angle 0.34364 ( 28) hydrogen bonds : bond 0.03102 ( 1226) hydrogen bonds : angle 4.04719 ( 3531) link_NAG-ASN : bond 0.00403 ( 7) link_NAG-ASN : angle 1.08996 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 446 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 MET cc_start: 0.8967 (mtm) cc_final: 0.8703 (mmm) REVERT: A 200 LEU cc_start: 0.8177 (mm) cc_final: 0.7668 (tt) REVERT: A 310 GLU cc_start: 0.7127 (tp30) cc_final: 0.6496 (pm20) REVERT: A 347 CYS cc_start: 0.9208 (m) cc_final: 0.8962 (m) REVERT: A 352 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 9 GLU cc_start: 0.8822 (tt0) cc_final: 0.8530 (tt0) REVERT: B 39 THR cc_start: 0.9072 (m) cc_final: 0.8809 (t) REVERT: B 200 LEU cc_start: 0.8195 (mm) cc_final: 0.7663 (tt) REVERT: B 256 ASP cc_start: 0.7253 (t70) cc_final: 0.6985 (t0) REVERT: B 310 GLU cc_start: 0.6922 (tp30) cc_final: 0.6501 (pm20) REVERT: B 337 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7680 (tm-30) REVERT: B 352 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8226 (mm-30) REVERT: C 200 LEU cc_start: 0.8132 (mm) cc_final: 0.7670 (tt) REVERT: C 337 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7607 (tm-30) REVERT: D 39 THR cc_start: 0.9084 (m) cc_final: 0.8838 (t) REVERT: D 143 MET cc_start: 0.8967 (mtm) cc_final: 0.8679 (mmm) REVERT: D 200 LEU cc_start: 0.8305 (mm) cc_final: 0.7743 (tt) REVERT: D 306 LEU cc_start: 0.7208 (mt) cc_final: 0.6609 (tt) REVERT: D 310 GLU cc_start: 0.6802 (tp30) cc_final: 0.6390 (pm20) REVERT: D 337 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7646 (tm-30) REVERT: D 347 CYS cc_start: 0.9104 (m) cc_final: 0.8804 (m) REVERT: D 352 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7961 (mm-30) REVERT: E 37 MET cc_start: 0.8775 (tpp) cc_final: 0.8209 (tmm) REVERT: E 89 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.7882 (mm110) REVERT: E 140 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9068 (ptpp) REVERT: E 200 LEU cc_start: 0.8259 (mm) cc_final: 0.7704 (tt) REVERT: E 217 ARG cc_start: 0.8853 (tpp-160) cc_final: 0.8316 (tpp-160) REVERT: E 310 GLU cc_start: 0.6850 (tp30) cc_final: 0.6413 (pm20) REVERT: E 337 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7626 (tm-30) REVERT: E 352 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8201 (tp30) REVERT: F 143 MET cc_start: 0.9139 (mmm) cc_final: 0.8927 (mmm) REVERT: F 200 LEU cc_start: 0.8242 (mm) cc_final: 0.7767 (tt) REVERT: F 230 TYR cc_start: 0.9002 (t80) cc_final: 0.8634 (t80) REVERT: F 310 GLU cc_start: 0.6925 (tp30) cc_final: 0.6627 (pm20) REVERT: F 337 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7719 (tm-30) REVERT: F 352 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7875 (mm-30) REVERT: G 35 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8142 (t0) REVERT: G 37 MET cc_start: 0.8480 (tpp) cc_final: 0.8086 (tmm) REVERT: G 57 GLU cc_start: 0.8286 (pm20) cc_final: 0.7233 (pm20) REVERT: G 140 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8997 (ptpp) REVERT: G 217 ARG cc_start: 0.8769 (mmp80) cc_final: 0.8376 (mmp80) REVERT: G 256 ASP cc_start: 0.7797 (t70) cc_final: 0.7272 (t0) REVERT: G 306 LEU cc_start: 0.6957 (mt) cc_final: 0.6466 (tt) REVERT: G 310 GLU cc_start: 0.6770 (tp30) cc_final: 0.6405 (pm20) REVERT: G 352 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7987 (mm-30) outliers start: 72 outliers final: 58 residues processed: 494 average time/residue: 0.1306 time to fit residues: 98.5235 Evaluate side-chains 497 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 435 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 166 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 222 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 125 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 353 ASN D 134 HIS E 89 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 353 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.121019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.098965 restraints weight = 40490.167| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.01 r_work: 0.3473 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18648 Z= 0.127 Angle : 0.655 8.822 25466 Z= 0.317 Chirality : 0.044 0.310 3115 Planarity : 0.004 0.037 3115 Dihedral : 3.876 22.787 2709 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.44 % Allowed : 26.28 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.18), residues: 2380 helix: 1.98 (0.14), residues: 1554 sheet: None (None), residues: 0 loop : -1.25 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 75 TYR 0.020 0.001 TYR E 10 PHE 0.011 0.001 PHE A 54 TRP 0.012 0.001 TRP E 104 HIS 0.006 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00295 (18627) covalent geometry : angle 0.65500 (25417) SS BOND : bond 0.00128 ( 14) SS BOND : angle 0.33448 ( 28) hydrogen bonds : bond 0.03073 ( 1226) hydrogen bonds : angle 4.06336 ( 3531) link_NAG-ASN : bond 0.00385 ( 7) link_NAG-ASN : angle 1.08507 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 445 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8489 (tpp) cc_final: 0.8033 (tmm) REVERT: A 143 MET cc_start: 0.8982 (mtm) cc_final: 0.8707 (mmm) REVERT: A 200 LEU cc_start: 0.8199 (mm) cc_final: 0.7685 (tt) REVERT: A 310 GLU cc_start: 0.7090 (tp30) cc_final: 0.6469 (pm20) REVERT: A 347 CYS cc_start: 0.9219 (m) cc_final: 0.8982 (m) REVERT: A 352 GLU cc_start: 0.8652 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 39 THR cc_start: 0.9054 (m) cc_final: 0.8783 (t) REVERT: B 140 LYS cc_start: 0.9358 (ptmt) cc_final: 0.9093 (ptmt) REVERT: B 200 LEU cc_start: 0.8198 (mm) cc_final: 0.7686 (tt) REVERT: B 256 ASP cc_start: 0.7250 (t70) cc_final: 0.6983 (t0) REVERT: B 310 GLU cc_start: 0.6946 (tp30) cc_final: 0.6546 (pm20) REVERT: B 337 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 352 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8017 (mm-30) REVERT: C 89 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8096 (mm110) REVERT: C 200 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7675 (tt) REVERT: D 143 MET cc_start: 0.8997 (mtm) cc_final: 0.8701 (mmm) REVERT: D 200 LEU cc_start: 0.8303 (mm) cc_final: 0.7729 (tt) REVERT: D 306 LEU cc_start: 0.7189 (mt) cc_final: 0.6603 (tt) REVERT: D 310 GLU cc_start: 0.6801 (tp30) cc_final: 0.6391 (pm20) REVERT: D 337 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7642 (tm-30) REVERT: D 352 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7923 (mm-30) REVERT: E 37 MET cc_start: 0.8736 (tpp) cc_final: 0.8246 (tmm) REVERT: E 89 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8221 (mm110) REVERT: E 140 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9063 (ptpp) REVERT: E 143 MET cc_start: 0.9092 (mtm) cc_final: 0.8797 (mmm) REVERT: E 200 LEU cc_start: 0.8226 (mm) cc_final: 0.7695 (tt) REVERT: E 310 GLU cc_start: 0.6857 (tp30) cc_final: 0.6441 (pm20) REVERT: E 337 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 352 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8180 (tp30) REVERT: F 200 LEU cc_start: 0.8264 (mm) cc_final: 0.7777 (tt) REVERT: F 230 TYR cc_start: 0.9014 (t80) cc_final: 0.8636 (t80) REVERT: F 256 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7101 (t0) REVERT: F 310 GLU cc_start: 0.6916 (tp30) cc_final: 0.6619 (pm20) REVERT: F 337 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7720 (tm-30) REVERT: F 352 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7896 (mm-30) REVERT: G 35 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8127 (t0) REVERT: G 37 MET cc_start: 0.8466 (tpp) cc_final: 0.8037 (tmm) REVERT: G 140 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8941 (ptpp) REVERT: G 217 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8385 (mmp80) REVERT: G 256 ASP cc_start: 0.7839 (t70) cc_final: 0.7325 (t0) REVERT: G 306 LEU cc_start: 0.6926 (mt) cc_final: 0.6461 (tt) REVERT: G 310 GLU cc_start: 0.6788 (tp30) cc_final: 0.6441 (pm20) REVERT: G 352 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8007 (mm-30) outliers start: 63 outliers final: 52 residues processed: 487 average time/residue: 0.1361 time to fit residues: 101.5892 Evaluate side-chains 498 residues out of total 2170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 439 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 140 LYS Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 305 VAL Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 134 HIS Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 305 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 54 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 210 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 87 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS B 353 ASN C 134 HIS C 353 ASN E 89 GLN E 134 HIS F 134 HIS F 353 ASN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 353 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.122252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100549 restraints weight = 40879.996| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.03 r_work: 0.3468 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18648 Z= 0.130 Angle : 0.661 8.974 25466 Z= 0.320 Chirality : 0.044 0.291 3115 Planarity : 0.004 0.037 3115 Dihedral : 3.876 23.581 2709 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.09 % Allowed : 25.52 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2380 helix: 2.00 (0.14), residues: 1554 sheet: None (None), residues: 0 loop : -1.24 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 128 TYR 0.014 0.001 TYR E 230 PHE 0.011 0.001 PHE A 54 TRP 0.010 0.001 TRP B 104 HIS 0.004 0.001 HIS F 134 Details of bonding type rmsd covalent geometry : bond 0.00303 (18627) covalent geometry : angle 0.66126 (25417) SS BOND : bond 0.00145 ( 14) SS BOND : angle 0.35045 ( 28) hydrogen bonds : bond 0.03080 ( 1226) hydrogen bonds : angle 4.05853 ( 3531) link_NAG-ASN : bond 0.00373 ( 7) link_NAG-ASN : angle 1.09363 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3743.72 seconds wall clock time: 65 minutes 21.71 seconds (3921.71 seconds total)